{"id":482,"date":"2016-05-30T11:21:12","date_gmt":"2016-05-30T09:21:12","guid":{"rendered":"http:\/\/vm-bioinfo-wp.toulouse.inra.fr\/?page_id=482"},"modified":"2023-05-10T08:11:02","modified_gmt":"2023-05-10T06:11:02","slug":"softwares","status":"publish","type":"page","link":"https:\/\/bioinfo.genotoul.fr\/index.php\/resources-2\/softwares\/","title":{"rendered":"Software"},"content":{"rendered":"<p>The GenoToul bioinformatics platform provides access to high-performance computing resources with softwares already installed to ease its usage. An exhaustive list is provided hereunder. <strong>Software are updated only upon user request.<\/strong> If you need any other software or if you need an update,\u00a0fill the <a href=\"https:\/\/bioinfo.genotoul.fr\/index.php\/help\/install-soft\/\">installation software\u00a0form<\/a>.<\/p>\n<p style=\"text-align: center;\">\u00a0<\/p>\n<hr \/>\n<div class=\"csRow\">\n<div class=\"csColumn\" style=\"margin: 0px; padding: 0px; float: left; width: 50%; text-align: left;\" data-csid=\"dc90e819-23b5-8fed-a304-7d80a1f169a6\" data-cswidth=\"50%\" data-csendpoint=\"472.4999987011719\" data-csstartpoint=\"14.999998701171876\">Select a category: \n<!-- Start Link Library Cats Time: 1775658986.0917-->\n<!-- Link Library Categories Output -->\n\n\n<!-- Category taxonomy: link_library_category -->\n\n\n<!-- Parent Cat ID: Array\n(\n)\n -->\n\n\n<!-- Category Query: Array\n(\n    [hide_empty] => 1\n    [orderby] => name\n    [order] => ASC\n)\n -->\n\n\n<!-- Category Results: Array\n(\n    [0] => 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0\n            [term_taxonomy_id] => 1118\n            [taxonomy] => link_library_category\n            [description] => \n            [parent] => 0\n            [count] => 53\n            [filter] => raw\n        )\n\n    [36] => WP_Term Object\n        (\n            [term_id] => 1142\n            [name] => Ribo-seq\n            [slug] => ribo-seq\n            [term_group] => 0\n            [term_taxonomy_id] => 1142\n            [taxonomy] => link_library_category\n            [description] => \n            [parent] => 0\n            [count] => 1\n            [filter] => raw\n        )\n\n    [37] => WP_Term Object\n        (\n            [term_id] => 1145\n            [name] => scDNA\n            [slug] => scdna\n            [term_group] => 0\n            [term_taxonomy_id] => 1145\n            [taxonomy] => link_library_category\n            [description] => \n            [parent] => 0\n            [count] => 4\n            [filter] => raw\n        )\n\n    [38] => WP_Term 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data-linklist-id='1'>\t<option value=\"#all-software\">All software<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#amplicon-analysis\">Amplicon analysis<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#annotation\">Annotation<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#assembly\">Assembly<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#atac-seq\">ATAC-Seq<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#bs-seq-analysis\">BS-seq analysis<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#chip-seq-analysis\">ChIP-seq analysis<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#database-querying\">Database querying<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#dna-and-protein-language-models\">DNA and protein language models<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#epigenetic\">Epigenetic<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#expression-analysis\">Expression analysis<span class=\"linkcatdesc\">RNA-Seq, ncRNA expression ...<\/span><\/option>\n\t<option value=\"#gene-fusion\">Gene fusion<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#genetic-map\">Genetic map<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#genetics\">Genetics<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#genomic-association-studies\">Genomic association studies<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#genotyping\">Genotyping<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#haplotypes\">Haplotypes<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#hic\">HiC<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#iso-seq-analysis\">Iso-seq analysis<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#librairies-and-other-tools\">Librairies and other tools<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#long-reads\">Long reads<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#mathematic\">Mathematics<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#metabolic-network-modeling\">Metabolic Network Modeling<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#metabolomics\">Metabolomics<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#ncrna\">ncRNA<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#nucleic-acid-folding\">Nucleic acid folding<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#ont\">ONT<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#pangenome\">Pangenome<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#patterns-and-profiles\">Patterns and profiles<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#phylogeny-selection-metagenomic\">Phylogeny &amp; selection \/ Metagenomic<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#population-genetics\">Population genetics<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#primers\">Primers<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#proteins\">Proteins<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#quality-and-cleaning\">Quality and cleaning<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#rad-seq-analysis\">RAD-seq analysis<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#repeats\">Repeats<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#ribo-seq\">Ribo-seq<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#scdna\">scDNA<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#sequences-alignment\">Sequences alignment<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#single-cell\">Single-cell<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#snp-and-structural-variations\">SNP and structural variations<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#systems-biology\">Systems biology<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#transcription-factors\">Transcription factors<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#visualization\">Visualization<span class=\"linkcatdesc\"><\/span><\/option>\n\t<option value=\"#workflow\">Workflow<span class=\"linkcatdesc\"><\/span><\/option>\n<\/select>\n<\/form><\/div>\n<script TYPE='text\/javascript'>\n\tfunction showcategory( catidvar ){\n\t\tlocation=\ndocument.catselect.catdropdown1.options[document.catselect.catdropdown1.selectedIndex].value }\n<\/script>\n\n<div style='clear:both' \/>\n\n<!-- End of Link Library Categories Output -->\n<!-- [link-library-cats] shortcode execution time: 0.0022521018981934-->\n<\/div>\n<div class=\"csColumn\" style=\"margin: 0px; padding: 0px; float: left; width: 50%; text-align: left;\" data-csid=\"0a66f741-95cc-8348-9618-ad7d015f0aa7\" data-cswidth=\"50%\" data-csendpoint=\"945.00002921875\" data-csstartpoint=\"487.50002921875\">Search a software: <form method=\"get\" id=\"llsearch\">\n<div>\n<input type='text' onfocus=\"this.value=''\" value='Search...' name='searchll' id='searchll' \/><input type='submit' id='searchbutton' value='Search' \/><\/div>\n<\/form>\n\n<script type='text\/javascript'>\njQuery(document).ready(function () {\n\tjQuery('#searchbutton').click(function () {\n\t\tif (jQuery('#searchll').val() == 'Search...') {\n\t\t\treturn false;\n\t\t}\n\t\telse {\n\t\t\tjQuery('#llsearch').submit();\n\t\t}\n\t});\n\tjQuery('#resetbutton').click(function () {\n\t\twindow.location.href = 'https:\/\/bioinfo.genotoul.fr\/index.php\/resources-2\/softwares\/';\n\t\treturn false;\n\t});\n});\n<\/script><\/div>\n<div style=\"clear: both; float: none; display: block; visibility: hidden; width: 0px; font-size: 0px; line-height: 0;\">\u00a0<\/div>\n<\/div>\n<hr \/>\n<p>&nbsp;<\/p>\n\n<!-- Library Settings Info:Array\n(\n    [num_columns] => 1\n    [showdescription] => \n    [shownotes] => 1\n    [beforenote] => <td>\n    [afternote] => <\/td>\n    [beforeitem] => <tr>\n    [afteritem] => <\/tr>\n    [beforedesc] => \n    [afterdesc] => \n    [displayastable] => true\n    [beforelink] => <td>\n    [afterlink] => <\/td>\n    [showcolumnheaders] => 1\n    [beforerss] => \n    [afterrss] => \n    [beforedate] => \n    [afterdate] => \n    [beforeimage] => <td>\n    [afterimage] => <\/td>\n    [beforeweblink] => \n    [afterweblink] => \n    [beforetelephone] => \n    [aftertelephone] => \n    [beforeemail] => \n    [afteremail] => \n    [beforelinkhits] => \n    [afterlinkhits] => \n    [columnheaderoverride] => Application,Description,Availability\/Use\n    [order] => name\n    [hide_if_empty] => 1\n    [table_width] => 100\n    [catanchor] => 1\n    [flatlist] => dropdowndirect\n    [categorylist_cpt] => \n    [excludecategorylist_cpt] => \n    [showrating] => \n    [showupdated] => \n    [show_images] => \n    [use_html_tags] => 1\n    [show_rss] => \n    [nofollow] => \n    [catlistwrappers] => 1\n    [beforecatlist1] => \n    [beforecatlist2] => \n    [beforecatlist3] => \n    [divorheader] => \n    [catnameoutput] => linklistcatname\n    [show_rss_icon] => \n    [linkaddfrequency] => 0\n    [addbeforelink] => \n    [addafterlink] => \n    [linktarget] => \n    [showcategorydescheaders] => 1\n    [showcategorydesclinks] => 1\n    [settingssetname] => Default\n    [showadmineditlinks] => 1\n    [showonecatonly] => \n    [loadingicon] => \/icons\/Ajax-loader.gif\n    [defaultsinglecat_cpt] => \n    [rsspreview] => \n    [rsspreviewcount] => 3\n    [rssfeedinline] => \n    [rssfeedinlinecontent] => \n    [rssfeedinlinecount] => 1\n    [rssfeedinlinedayspublished] => 90\n    [rssfeedinlineskipempty] => \n    [direction] => ASC\n    [linkdirection] => ASC\n    [linkorder] => name\n    [pagination] => \n    [linksperpage] => 5\n    [hidecategorynames] => \n    [showinvisible] => \n    [showinvisibleadmin] => \n    [showdate] => \n    [catdescpos] => right\n    [catlistdescpos] => right\n    [showuserlinks] => \n    [addnewlinkmsg] => Add new link\n    [linknamelabel] => Link name\n    [linkaddrlabel] => Link address\n    [linkrsslabel] => Link RSS\n    [linkcatlabel] => Link Category\n    [linkdesclabel] => Link Description\n    [linknoteslabel] => Link Notes\n    [addlinkbtnlabel] => Add Link\n    [newlinkmsg] => New link submitted.\n    [moderatemsg] => It will appear in the list once moderated. Thank you.\n    [rsspreviewwidth] => 900\n    [rsspreviewheight] => 700\n    [imagepos] => beforename\n    [imageclass] => \n    [emailnewlink] => \n    [emailsubmitter] => \n    [showaddlinkrss] => hide\n    [showaddlinkdesc] => hide\n    [showaddlinkcat] => hide\n    [showaddlinknotes] => hide\n    [usethumbshotsforimages] => \n    [uselocalimagesoverthumbshots] => \n    [addlinkreqlogin] => \n    [showcatlinkcount] => \n    [publishrssfeed] => \n    [numberofrssitems] => 10\n    [rssfeedtitle] => Link Library-Generated RSS Feed\n    [rssfeeddescription] => Description of Link Library-Generated Feed\n    [showonecatmode] => AJAX\n    [paginationposition] => AFTER\n    [addlinkcustomcat] => hide\n    [linkcustomcatlabel] => User-submitted category\n    [linkcustomcatlistentry] => User-submitted category (define below)\n    [searchlabel] => Search\n    [dragndroporder] => 2,12,5,1,3,4,6,7,8,9,10,11,13,14,15,16,17,23\n    [showname] => 1\n    [cattargetaddress] => \n    [displayweblink] => false\n    [sourceweblink] => primary\n    [showtelephone] => false\n    [sourcetelephone] => primary\n    [showemail] => false\n    [showlinkhits] => \n    [weblinklabel] => \n    [telephonelabel] => \n    [emaillabel] => \n    [showaddlinkreciprocal] => hide\n    [linkreciprocallabel] => Reciprocal Link\n    [showaddlinksecondurl] => hide\n    [linksecondurllabel] => Secondary Address\n    [showaddlinktelephone] => hide\n    [linktelephonelabel] => Telephone\n    [showaddlinkemail] => hide\n    [linkemaillabel] => E-mail\n    [emailcommand] => \n    [sourceimage] => primary\n    [sourcename] => primary\n    [tooltipname] => no_tooltip\n    [enablerewrite] => \n    [rewritepage] => \n    [storelinksubmitter] => \n    [maxlinks] => \n    [showcaptcha] => \n    [beforelinkrating] => \n    [afterlinkrating] => \n    [linksubmitternamelabel] => Submitter Name\n    [showlinksubmittername] => hide\n    [linksubmitteremaillabel] => Submitter E-mail\n    [showaddlinksubmitteremail] => hide\n    [linksubmittercommentlabel] => Submitter Comment\n    [showlinksubmittercomment] => hide\n    [addlinkcatlistoverride] => \n    [showlargedescription] => 1\n    [beforelargedescription] => <td>\n    [afterlargedescription] => <\/td>\n    [showcustomcaptcha] => hide\n    [customcaptchaquestion] => Is boiling water hot or cold?\n    [customcaptchaanswer] => hot\n    [rssfeedaddress] => \n    [addlinknoaddress] => \n    [featuredfirst] => \n    [showlinksonclick] => \n    [linklargedesclabel] => Large Description\n    [showuserlargedescription] => hide\n    [usetextareaforusersubmitnotes] => \n    [showcatonsearchresults] => 1\n    [shownameifnoimage] => \n    [searchresultsaddress] => \n    [enable_link_popup] => \n    [link_popup_text] => %link_image%<br \/>Click through to visit %link_name%.\n    [popup_width] => 300\n    [popup_height] => 400\n    [nocatonstartup] => \n    [linktitlecontent] => linkdesc\n    [singlelinkid] => \n    [combineresults] => \n    [showifreciprocalvalid] => \n    [cat_letter_filter] => no\n    [cat_letter_filter_autoselect] => 1\n    [cat_letter_filter_showalloption] => 1\n    [beforefirstlink] => \n    [afterlastlink] => \n    [searchfieldtext] => Search...\n    [searchnoresultstext] => No links found matching your search criteria\n    [catfilterlabel] => Category Filter\n    [addlinkdefaultcat] => nodefaultcat\n    [addlinkakismet] => \n    [current_user_links] => \n    [showsubmittername] => \n    [beforesubmittername] => \n    [aftersubmittername] => \n    [onereciprocaldomain] => \n    [nooutputempty] => \n    [showcatdesc] => \n    [beforecatdesc] => \n    [aftercatdesc] => \n    [emailextracontent] => \n    [showparentcatname] => \n    [showparentcatdesc] => \n    [hidechildcatlinks] => \n    [childcatdepthlimit] => 0\n    [hidechildcattop] => \n    [catlinkspermalinksmode] => \n    [toppagetext] => \n    [showbreadcrumbspermalinks] => \n    [showlinktags] => \n    [beforelinktags] => \n    [afterlinktags] => \n    [showlinkprice] => \n    [beforelinkprice] => \n    [afterlinkprice] => \n    [linkcurrency] => $\n    [linkcurrencyplacement] => before\n    [show0asfree] => 1\n    [allowcolumnsorting] => \n    [extraquerystring] => \n    [updatedlabel] => New\n    [showupdatedpos] => before\n    [showsearchreset] => \n    [weblinktarget] => \n    [linktagslabel] => Link Tags\n    [showaddlinktags] => hide\n    [addlinktaglistoverride] => \n    [linkcustomtaglabel] => \n    [addlinkcustomtag] => hide\n    [linkcustomtaglistentry] => User-submitted tag (define below)\n    [showscheduledlinks] => \n    [maxlinkspercat] => \n    [suppressnoreferrer] => \n    [linkaddrdefvalue] => https:\/\/\n    [userlinkcatselectionlabel] => Select a category\n    [dropdownselectionprompt] => \n    [dropdownselectionprompttext] => Select a category\n    [showcatname] => \n    [beforecatname] => \n    [aftercatname] => \n    [onelinkperdomain] => \n    [showupdatedtooltip] => \n    [linkimagelabel] => Link Image (jpg, jpeg, png)\n    [showaddlinkimage] => hide\n    [datesource] => linkupdated\n    [taglist_cpt] => \n    [excludetaglist_cpt] => \n    [taglinks] => inactive\n    [catlistchildcatdepthlimit] => \n    [linknametooltip] => \n    [linkaddrtooltip] => \n    [linkrsstooltip] => \n    [linkcattooltip] => \n    [linkusercattooltip] => \n    [linktagtooltip] => \n    [linkusertagtooltip] => \n    [linkdesctooltip] => \n    [linknotestooltip] => \n    [linkimagetooltip] => \n    [linkreciptooltip] => \n    [linksecondtooltip] => \n    [linktelephonetooltip] => \n    [linkemailtooltip] => \n    [submitternametooltip] => \n    [submitteremailtooltip] => \n    [submittercommenttooltip] => \n    [largedesctooltip] => \n    [linkfilelabel] => \n    [linkfiletooltip] => \n    [showaddlinkfile] => hide\n    [linkfileallowedtypes] => pdf,zip\n    [displaycustomurl1] => false\n    [displaycustomurl2] => false\n    [displaycustomurl3] => false\n    [displaycustomurl4] => false\n    [displaycustomurl5] => false\n    [beforecustomurl1] => \n    [beforecustomurl2] => \n    [beforecustomurl3] => \n    [beforecustomurl4] => \n    [beforecustomurl5] => \n    [aftercustomurl1] => \n    [aftercustomurl2] => \n    [aftercustomurl3] => \n    [aftercustomurl4] => \n    [aftercustomurl5] => \n    [labelcustomurl1] => \n    [labelcustomurl2] => \n    [labelcustomurl3] => \n    [labelcustomurl4] => \n    [labelcustomurl5] => \n    [customurl1target] => \n    [customurl2target] => \n    [customurl3target] => \n    [customurl4target] => \n    [customurl5target] => \n    [searchtextinsearchbox] => \n    [showuservotes] => \n    [beforeuservotes] => \n    [afteruservotes] => \n    [membersonlylinkvotes] => \n    [uservotelikelabel] => Like\n    [searchfiltercats] => 1\n    [displaycustomtext1] => false\n    [displaycustomtext2] => false\n    [displaycustomtext3] => false\n    [displaycustomtext4] => false\n    [displaycustomtext5] => false\n    [beforecustomtext1] => \n    [beforecustomtext2] => \n    [beforecustomtext3] => \n    [beforecustomtext4] => \n    [beforecustomtext5] => \n    [aftercustomtext1] => \n    [aftercustomtext2] => \n    [aftercustomtext3] => \n    [aftercustomtext4] => \n    [aftercustomtext5] => \n    [displaycustomlist1] => false\n    [displaycustomlist2] => false\n    [displaycustomlist3] => false\n    [displaycustomlist4] => false\n    [displaycustomlist5] => false\n    [beforecustomlist1] => \n    [beforecustomlist2] => \n    [beforecustomlist3] => \n    [beforecustomlist4] => \n    [beforecustomlist5] => \n    [aftercustomlist1] => \n    [aftercustomlist2] => \n    [aftercustomlist3] => \n    [aftercustomlist4] => \n    [aftercustomlist5] => \n    [lazyloadimages] => \n    [emailhidepluginmessage] => \n    [suppress_image_if_empty] => \n    [suppress_link_date_if_empty] => \n    [suppress_link_desc_if_empty] => \n    [suppress_link_notes_if_empty] => \n    [suppress_rss_icon_if_empty] => \n    [suppress_tel_if_empty] => \n    [suppress_email_if_empty] => \n    [suppress_rating_if_empty] => \n    [suppress_large_desc_if_empty] => \n    [suppress_submitter_if_empty] => \n    [suppress_cat_desc_if_empty] => \n    [suppress_link_tags_if_empty] => \n    [suppress_link_price_if_empty] => \n    [suppress_cat_name_if_empty] => \n    [suppress_custom_url_1_if_empty] => \n    [suppress_custom_url_2_if_empty] => \n    [suppress_custom_url_3_if_empty] => \n    [suppress_custom_url_4_if_empty] => \n    [suppress_custom_url_5_if_empty] => \n    [suppress_custom_text_1_if_empty] => \n    [suppress_custom_text_2_if_empty] => \n    [suppress_custom_text_3_if_empty] => \n    [suppress_custom_text_4_if_empty] => \n    [suppress_custom_text_5_if_empty] => \n    [suppress_custom_list_1_if_empty] => \n    [suppress_custom_list_2_if_empty] => \n    [suppress_custom_list_3_if_empty] => \n    [suppress_custom_list_4_if_empty] => \n    [suppress_custom_list_5_if_empty] => \n    [catnameformat] => currentcatname\n    [catnamelink] => 1\n    [categoryseparator] =>  | \n    [customqueryarg] => \n    [customqueryargvalue] => \n    [usersubmissiondragndroporder] => 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33\n    [showlinkreferencelist] => hide\n    [linkreferencelabel] => Link Reference\n    [linkreferencetooltip] => \n    [showcustomurl1] => hide\n    [showcustomurl2] => hide\n    [showcustomurl3] => hide\n    [showcustomurl4] => hide\n    [showcustomurl5] => hide\n    [customurl1tooltip] => \n    [customurl2tooltip] => \n    [customurl3tooltip] => \n    [customurl4tooltip] => \n    [customurl5tooltip] => \n    [showcustomtext1] => hide\n    [showcustomtext2] => hide\n    [showcustomtext3] => hide\n    [showcustomtext4] => hide\n    [showcustomtext5] => hide\n    [customtext1tooltip] => \n    [customtext2tooltip] => \n    [customtext3tooltip] => \n    [customtext4tooltip] => \n    [customtext5tooltip] => \n    [showcustomlist1] => hide\n    [showcustomlist2] => hide\n    [showcustomlist3] => hide\n    [showcustomlist4] => hide\n    [showcustomlist5] => hide\n    [customlist1tooltip] => \n    [customlist2tooltip] => \n    [customlist3tooltip] => \n    [customlist4tooltip] => \n    [customlist5tooltip] => \n    [stylesheet] => \n    [rss_item_date_source] => updated_date\n    [hideemptycats] => 1\n    [rsslibraryitemspersite] => 10\n    [rsslibrarymaxwordsitem] => 30\n    [rsslibrarypagination] => 1\n    [rsslibrarypaginationnb] => 10\n    [rsslibrarytemplate] => <div class=\"rss_library_item\">\r\n\t<div class=\"rss-library-title\">[rss_item_title]<\/div>\r\n\t<div class=\"rss-library-source\"><span class=\"rss-library-site\">[link_title]<\/span><span class=\"rss-library-date\">[rss_item_date] - [rss_item_time]<\/span><\/div>\r\n\t<div class=\"rss-library-content\">[rss_item_content]<\/div>\r\n<\/div>\n    [showupdatedonly] => \n    [updateddays] => 7\n    [searchfromallcats] => \n    [suppressonemptysearch] => \n    [link_name] => 3D-DNA\n    [link_url] => https:\/\/github.com\/theaidenlab\/3d-dna\n    [link_rss] => \n    [link_description] => \n    [link_notes] => [strong]SLURM Cluster: [\/strong] [a href=index.php\/how-to-use?software=How_to_use_SLURM_3D-DNA] How to use [\/a]\n    [cat_name] => All software,Assembly\n    [link_visible] => Y\n    [link_second_url] => \n    [link_telephone] => \n    [link_email] => \n    [link_reciprocal] => \n    [link_image] => \n    [link_textfield] => 3D de novo assembly (3D-DNA) pipeline.\n    [link_no_follow] => \n    [link_rating] => 0\n    [link_target] => _blank\n    [link_updated] => 2020-12-04 15:24:25\n    [AJAXcatid] => \n    [AJAXpageid] => \n)\n-->\n\n<!-- Start Time: 1775658986.2847-->\n<!-- Beginning of Link Library Output --><div id='linklist1' class='linklist'><!-- Div Linklist -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1116\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [field] => term_id\n                            [terms] => 1116\n                            [include_children] => \n                        )\n\n                )\n\n            [post_status] => Array\n                (\n                    [0] => publish\n                )\n\n            [orderby] => Array\n                (\n                    [title] => ASC\n                )\n\n        )\n\n    [query_vars] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [field] => term_id\n                            [terms] => 1116\n                            [include_children] => \n                        )\n\n                )\n\n            [post_status] => Array\n                (\n                    [0] => publish\n                )\n\n            [orderby] => Array\n                (\n                    [title] => ASC\n                )\n\n            [error] => \n            [m] => \n            [p] => 0\n            [post_parent] => \n            [subpost] => \n            [subpost_id] => \n            [attachment] => \n            [attachment_id] => 0\n            [name] => \n            [pagename] => \n            [page_id] => 0\n            [second] => \n            [minute] => \n            [hour] => \n            [day] => 0\n            [monthnum] => 0\n            [year] => 0\n            [w] => 0\n            [category_name] => \n            [tag] => \n            [cat] => \n            [tag_id] => \n            [author] => \n            [author_name] => \n            [feed] => \n            [tb] => \n            [paged] => 0\n            [meta_key] => \n            [meta_value] => \n            [preview] => \n            [s] => \n            [sentence] => \n            [title] => \n            [fields] => \n            [menu_order] => \n            [embed] => \n            [category__in] => Array\n                (\n                )\n\n            [category__not_in] => Array\n                (\n                )\n\n            [category__and] => Array\n                (\n                )\n\n            [post__in] => Array\n                (\n                )\n\n            [post__not_in] => Array\n                (\n                )\n\n            [post_name__in] => Array\n                (\n                )\n\n            [tag__in] => Array\n                (\n                )\n\n            [tag__not_in] => Array\n                (\n                )\n\n            [tag__and] => Array\n                (\n                )\n\n            [tag_slug__in] => Array\n                (\n                )\n\n            [tag_slug__and] => Array\n                (\n                )\n\n            [post_parent__in] => Array\n                (\n                )\n\n            [post_parent__not_in] => Array\n                (\n                )\n\n            [author__in] => Array\n                (\n                )\n\n            [author__not_in] => Array\n                (\n                )\n\n            [ignore_sticky_posts] => \n            [suppress_filters] => \n            [cache_results] => 1\n            [update_post_term_cache] => 1\n            [update_menu_item_cache] => \n            [lazy_load_term_meta] => 1\n            [update_post_meta_cache] => 1\n            [nopaging] => 1\n            [comments_per_page] => 50\n            [no_found_rows] => \n            [taxonomy] => link_library_category\n            [term_id] => 1116\n            [order] => DESC\n        )\n\n    [tax_query] => WP_Tax_Query Object\n        (\n            [queries] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [terms] => Array\n                                (\n                                    [0] => 1116\n                                )\n\n                            [field] => term_id\n                            [operator] => IN\n                            [include_children] => \n                        )\n\n                )\n\n            [relation] => AND\n            [table_aliases:protected] => Array\n                (\n                    [0] => wp_term_relationships\n                )\n\n            [queried_terms] => Array\n                (\n                    [link_library_category] => Array\n                        (\n                            [terms] => Array\n                                (\n                                    [0] => 1116\n                                )\n\n                            [field] => term_id\n                        )\n\n                )\n\n            [primary_table] => wp_posts\n            [primary_id_column] => ID\n        )\n\n    [meta_query] => WP_Meta_Query Object\n        (\n            [queries] => Array\n                (\n                )\n\n            [relation] => \n            [meta_table] => \n            [meta_id_column] => \n            [primary_table] => \n            [primary_id_column] => \n            [table_aliases:protected] => Array\n                (\n                )\n\n            [clauses:protected] => Array\n                (\n                )\n\n            [has_or_relation:protected] => \n        )\n\n    [date_query] => \n    [request] => \n\t\t\tSELECT   wp_posts.*\n\t\t\tFROM wp_posts  LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1116)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 24131\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:58\n                    [post_date_gmt] => 2022-11-22 09:25:58\n                    [post_content] => \n                    [post_title] => 3D-DNA\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => 3d-dna\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:20:14\n                    [post_modified_gmt] => 2025-05-21 05:20:14\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/3d-dna\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 25351\n                    [post_author] => 5\n                    [post_date] => 2024-04-22 15:06:18\n                    [post_date_gmt] => 2024-04-22 13:06:18\n                    [post_content] => \n                    [post_title] => 3rdChimeraMiner\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => 3rdchimeraminer\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-03 09:16:10\n                    [post_modified_gmt] => 2024-06-03 07:16:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25351\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 24132\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:55\n                    [post_date_gmt] => 2022-11-22 09:25:55\n                    [post_content] => \n                    [post_title] => AAF\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => aaf\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:20:23\n                    [post_modified_gmt] => 2025-05-21 05:20:23\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/aaf\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 23836\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:39\n                    [post_date_gmt] => 2022-11-22 09:25:39\n                    [post_content] => \n                    [post_title] => ABCtoolbox\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => abctoolbox\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:20:41\n                    [post_modified_gmt] => 2025-05-21 05:20:41\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/abctoolbox\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [4] => WP_Post Object\n                (\n                    [ID] => 23578\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:28\n                    [post_date_gmt] => 2022-11-22 09:25:28\n                    [post_content] => \n                    [post_title] => ABySS\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => abyss\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:20:44\n                    [post_modified_gmt] => 2025-05-21 05:20:44\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/abyss\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [5] => WP_Post Object\n                (\n                    [ID] => 23939\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:44\n                    [post_date_gmt] => 2022-11-22 09:25:44\n                    [post_content] => \n                    [post_title] => AC-DIAMOND\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => ac-diamond\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:20:48\n                    [post_modified_gmt] => 2025-05-21 05:20:48\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/ac-diamond\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [6] => WP_Post Object\n                (\n                    [ID] => 25395\n                    [post_author] => 5\n                    [post_date] => 2024-05-06 08:41:08\n                    [post_date_gmt] => 2024-05-06 06:41:08\n                    [post_content] => \n                    [post_title] => ACACIA\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => acacia\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-17 08:39:43\n                    [post_modified_gmt] => 2024-06-17 06:39:43\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25395\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [7] => WP_Post Object\n                (\n                    [ID] => 24133\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:57\n                    [post_date_gmt] => 2022-11-22 09:25:57\n                    [post_content] => \n                    [post_title] => Accel-align\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => accel-align\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:21:08\n                    [post_modified_gmt] => 2025-05-21 05:21:08\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/accel-align\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [8] => WP_Post Object\n                (\n                    [ID] => 23905\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:42\n                    [post_date_gmt] => 2022-11-22 09:25:42\n                    [post_content] => \n                    [post_title] => ACFS\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => acfs\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:21:14\n                    [post_modified_gmt] => 2025-05-21 05:21:14\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/acfs\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [9] => WP_Post Object\n                (\n                    [ID] => 26021\n                    [post_author] => 5\n                    [post_date] => 2025-07-17 07:20:23\n                    [post_date_gmt] => 2025-07-17 05:20:23\n                    [post_content] => \n                    [post_title] => AdamaJava\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => adamajava\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-08-04 15:42:37\n                    [post_modified_gmt] => 2025-08-04 13:42:37\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26021\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [10] => WP_Post Object\n                (\n                    [ID] => 23579\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => AdapterRemoval\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => adapterremoval\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:21:18\n                    [post_modified_gmt] => 2025-05-21 05:21:18\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/adapterremoval\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 24134\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:54\n                    [post_date_gmt] => 2022-11-22 09:25:54\n                    [post_content] => \n                    [post_title] => adegenet\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => adegenet\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:21:21\n                    [post_modified_gmt] => 2025-05-21 05:21:21\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/adegenet\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [12] => WP_Post Object\n                (\n                    [ID] => 23580\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => ADMIXTOOLS\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => admixtools\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:22:18\n                    [post_modified_gmt] => 2025-05-21 05:22:18\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/admixtools\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [13] => WP_Post Object\n                (\n                    [ID] => 23581\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => Admixture\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => admixture\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:22:25\n                    [post_modified_gmt] => 2025-05-21 05:22:25\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/admixture\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [14] => WP_Post Object\n                (\n                    [ID] => 24135\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:59\n                    [post_date_gmt] => 2022-11-22 09:25:59\n                    [post_content] => \n                    [post_title] => AGAT\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => agat\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:22:29\n                    [post_modified_gmt] => 2025-05-21 05:22:29\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/agat\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [15] => WP_Post Object\n                (\n                    [ID] => 26219\n                    [post_author] => 5\n                    [post_date] => 2026-02-17 09:40:53\n                    [post_date_gmt] => 2026-02-17 08:40:53\n                    [post_content] => \n                    [post_title] => AGC\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => agc\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-03-09 09:17:01\n                    [post_modified_gmt] => 2026-03-09 08:17:01\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26219\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [16] => WP_Post Object\n                (\n                    [ID] => 23582\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => ALDER\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alder\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:24:08\n                    [post_modified_gmt] => 2025-05-21 05:24:08\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/alder\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [17] => WP_Post Object\n                (\n                    [ID] => 25570\n                    [post_author] => 5\n                    [post_date] => 2024-10-28 14:12:20\n                    [post_date_gmt] => 2024-10-28 13:12:20\n                    [post_content] => \n                    [post_title] => ALFATClust\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alfatclust\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-11-20 11:37:56\n                    [post_modified_gmt] => 2024-11-20 10:37:56\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25570\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [18] => WP_Post Object\n                (\n                    [ID] => 23978\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:45\n                    [post_date_gmt] => 2022-11-22 09:25:45\n                    [post_content] => \n                    [post_title] => Alfred\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alfred\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:22:40\n                    [post_modified_gmt] => 2025-05-21 05:22:40\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/alfred\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [19] => WP_Post Object\n                (\n                    [ID] => 23801\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:38\n                    [post_date_gmt] => 2022-11-22 09:25:38\n                    [post_content] => \n                    [post_title] => AlleleSeq\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alleleseq\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:23:02\n                    [post_modified_gmt] => 2025-05-21 05:23:02\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/alleleseq\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [20] => WP_Post Object\n                (\n                    [ID] => 24136\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:54\n                    [post_date_gmt] => 2022-11-22 09:25:54\n                    [post_content] => \n                    [post_title] => ALLHiC\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => allhic\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:23:48\n                    [post_modified_gmt] => 2025-05-21 05:23:48\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/allhic\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [21] => WP_Post Object\n                (\n                    [ID] => 23583\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => AllPaths-LG\n                    [post_excerpt] => \n                    [post_status] => publish\n                    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[post_title] => 3D-DNA\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => 3d-dna\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2025-05-21 07:20:14\n            [post_modified_gmt] => 2025-05-21 05:20:14\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/3d-dna\/\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 1314\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    [is_category] => \n    [is_tag] => \n    [is_tax] => 1\n    [is_search] => \n    [is_feed] => \n    [is_comment_feed] => \n    [is_trackback] => \n    [is_home] => \n    [is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => 7e2c68dc3b5fa1dcf3fe61d6402440bc\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.020869970321655-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1116 level0\"><!-- Div Category --><div id=\"all-software\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">All software<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/theaidenlab\/3d-dna\" id=\"link-24131\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">3D-DNA<\/a>\n<!-- Time to render name section of link id 24131: 3.0994415283203E-6 --> \n<\/td>\n<td><p>3D de novo assembly (3D-DNA) pipeline.<\/p>\n<!-- Time to render link large description section of link id 24131: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_3D-DNA> How to use <\/a>\n<!-- Time to render notes section of link id 24131: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24131: 0.00022697448730469 --> \n<tr><td><a href=\"https:\/\/github.com\/dulunar\/3rdChimeraMiner\" id=\"link-25351\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">3rdChimeraMiner<\/a>\n<!-- Time to render name section of link id 25351: 3.0994415283203E-6 --> \n<\/td>\n<td>Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.\n<!-- Time to render link large description section of link id 25351: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_3rdChimeraMiner> How to use <\/a>\n<!-- Time to render notes section of link id 25351: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25351: 0.0001978874206543 --> \n<tr><td><a href=\"https:\/\/github.com\/fanhuan\/AAF\" id=\"link-24132\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AAF<\/a>\n<!-- Time to render name section of link id 24132: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This is a package for constructing phylogeny without doing alignment or assembly.<\/p>\n<!-- Time to render link large description section of link id 24132: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24132: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24132: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/wegmannlab\/abctoolbox\/src\/master\/\" id=\"link-23836\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ABCtoolbox<\/a>\n<!-- Time to render name section of link id 23836: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BCtoolbox is a general-purpose program to perform Approximate Bayesian Computation. ABCtoolbox can be used for ABC inference on almost any type of model, including models arising in physics, biology or engineering.<\/p>\n<!-- Time to render link large description section of link id 23836: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23836: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23836: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/www.bcgsc.ca\/platform\/bioinfo\/software\/abyss\" id=\"link-23578\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ABySS<\/a>\n<!-- Time to render name section of link id 23578: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads.<\/p>\n<!-- Time to render link large description section of link id 23578: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ABySS> How to use <\/a>\n<!-- Time to render notes section of link id 23578: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23578: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/Maihj\/AC-DIAMOND\/\" id=\"link-23939\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AC-DIAMOND<\/a>\n<!-- Time to render name section of link id 23939: 3.0994415283203E-6 --> \n<\/td>\n<td><p>AC-DIAMOND attempts to speed up DIAMOND via better SIMD parallelization and compressed indexing. Experimental results show that AC-DIAMOND was about 6~7 times faster than DIAMOND on aligning DNA reads or contigs while retaining the essentially the similar sensitivity. AC-DIAMOND was developped based on DIAMOND v0.7.9.<\/p>\n<!-- Time to render link large description section of link id 23939: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23939: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23939: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/psc_santos\/ACACIA\" id=\"link-25395\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ACACIA<\/a>\n<!-- Time to render name section of link id 25395: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Allele CAlling proCedure for Illumina Amplicon sequencing data: This workflow aims at extracting allele information out of paired-end Illumina FASTQC files.<\/p>\n<!-- Time to render link large description section of link id 25395: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ACACIA> How to use <\/a>\n<!-- Time to render notes section of link id 25395: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25395: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/raja-appuswamy\/accel-align-release\" id=\"link-24133\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Accel-align<\/a>\n<!-- Time to render name section of link id 24133: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Accel-align is a fast alignment tool implemented in C++ programming language.<\/p>\n<!-- Time to render link large description section of link id 24133: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24133: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24133: 0.0001680850982666 --> \n<tr><td><a href=\"https:\/\/github.com\/arthuryxt\/acfs\" id=\"link-23905\" class=\"track_this_link \" rel=\"noopener noreferrer\">ACFS<\/a>\n<!-- Time to render name section of link id 23905: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Accurate CircRNA Finder Suite. Discovering circRNAs from RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 23905: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23905: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23905: 0.00023102760314941 --> \n<tr><td><a href=\"https:\/\/github.com\/AdamaJava\/adamajava\" id=\"link-26021\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AdamaJava<\/a>\n<!-- Time to render name section of link id 26021: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).<\/p>\n<!-- Time to render link large description section of link id 26021: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AdamaJava> How to use <\/a>\n<!-- Time to render notes section of link id 26021: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26021: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/MikkelSchubert\/adapterremoval\" id=\"link-23579\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AdapterRemoval<\/a>\n<!-- Time to render name section of link id 23579: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This program was developed to remove residual adapter sequences from next generation sequencing reads. The program handles both single end and paired end data.<\/p>\n<!-- Time to render link large description section of link id 23579: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AdapterRemoval> How to use <\/a>\n<!-- Time to render notes section of link id 23579: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23579: 0.00019502639770508 --> \n<tr><td><a href=\"http:\/\/adegenet.r-forge.r-project.org\" id=\"link-24134\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">adegenet<\/a>\n<!-- Time to render name section of link id 24134: 2.1457672119141E-6 --> \n<\/td>\n<td><p>R package dedicated to the exploratory analysis of genetic data. It implements a set of tools ranging from multivariate methods to spatial genetics and genome-wise SNP data analysis<\/p>\n<!-- Time to render link large description section of link id 24134: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24134: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24134: 0.00018191337585449 --> \n<tr><td><a href=\"http:\/\/genetics.med.harvard.edu\/reich\/Reich_Lab\/Software.html\" id=\"link-23580\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ADMIXTOOLS<\/a>\n<!-- Time to render name section of link id 23580: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.<\/p>\n<!-- Time to render link large description section of link id 23580: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ADMIXTOOLS> How to use <\/a>\n<!-- Time to render notes section of link id 23580: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23580: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/dalexander.github.io\/admixture\/\" id=\"link-23581\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Admixture<\/a>\n<!-- Time to render name section of link id 23581: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.<\/p>\n<!-- Time to render link large description section of link id 23581: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ADMIXTURE> How to use <\/a>\n<!-- Time to render notes section of link id 23581: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23581: 0.00016617774963379 --> \n<tr><td><a href=\"https:\/\/github.com\/NBISweden\/AGAT\" id=\"link-24135\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AGAT<\/a>\n<!-- Time to render name section of link id 24135: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Another Gff Analysis Toolkit: suite of tools to handle gene annotations in any GTF\/GFF format. Some examples what AGAT can do: standardise any GTF\/GFF file into a comprehensive GFF3 format (script with agat_sp prefix): add missing parent features (e.g. gene and mRNA if only CDS\/exon exist). add missing features (e.g. exon and UTR). add missing mandatory attributes (i.e. ID, Parent). fix identifier to be uniq. fix feature location. remove duplicated features. group related features (if spread in different places in the file). sort features. merge overlapping loci into one single locus (only if option activated).<\/p>\n<!-- Time to render link large description section of link id 24135: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AGAT> How to use <\/a>\n<!-- Time to render notes section of link id 24135: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24135: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/refresh-bio\/agc\" id=\"link-26219\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AGC<\/a>\n<!-- Time to render name section of link id 26219: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans).<\/p>\n<!-- Time to render link large description section of link id 26219: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AGC> How to use <\/a>\n<!-- Time to render notes section of link id 26219: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26219: 0.00016307830810547 --> \n<tr><td><a href=\"http:\/\/groups.csail.mit.edu\/cb\/alder\/\" id=\"link-23582\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ALDER<\/a>\n<!-- Time to render name section of link id 23582: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture<\/p>\n<!-- Time to render link large description section of link id 23582: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23582: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23582: 0.00016093254089355 --> \n<tr><td><a href=\"https:\/\/github.com\/phglab\/ALFATClust\" id=\"link-25570\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ALFATClust<\/a>\n<!-- Time to render name section of link id 25570: 2.1457672119141E-6 --> \n<\/td>\n<td>ALignment-Free Adaptive Threshold Clustering:Biological sequence clustering tool with dynamic threshold for individual clusters. Suitable for clustering multiple groups of homologous sequences.\n<!-- Time to render link large description section of link id 25570: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ALFATClust> How to use <\/a>\n<!-- Time to render notes section of link id 25570: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25570: 0.00019717216491699 --> \n<tr><td><a href=\"https:\/\/github.com\/tobiasrausch\/alfred\" id=\"link-23978\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Alfred<\/a>\n<!-- Time to render name section of link id 23978: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BAM Statistics, Feature Counting and Annotation<\/p>\n<!-- Time to render link large description section of link id 23978: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23978: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23978: 0.0001828670501709 --> \n<tr><td><a href=\"http:\/\/alleleseq.gersteinlab.org\/tools.html\" id=\"link-23801\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlleleSeq<\/a>\n<!-- Time to render name section of link id 23801: 1.9073486328125E-6 --> \n<\/td>\n<td><p>pipeline which constructs a diploid personal genome from genomic sequence variants of a family trio, including SNPs, indels and structural variants and maps functional genomic data onto this personal genome.<\/p>\n<!-- Time to render link large description section of link id 23801: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23801: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23801: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/tangerzhang\/ALLHiC\" id=\"link-24136\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ALLHiC<\/a>\n<!-- Time to render name section of link id 24136: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Phasing and scaffolding polyploid genomes based on Hi-C data<\/p>\n<!-- Time to render link large description section of link id 24136: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ALLHiC> How to use <\/a>\n<!-- Time to render notes section of link id 24136: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24136: 0.00017714500427246 --> \n<tr><td><a href=\"http:\/\/software.broadinstitute.org\/allpaths-lg\/blog\/\" id=\"link-23583\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AllPaths-LG<\/a>\n<!-- Time to render name section of link id 23583: 2.8610229492188E-6 --> \n<\/td>\n<td><p>ALLPATHS-LG is a whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. The significant difference between ALLPATHS and traditional assemblers such as Arachne is that ALLPATHS assemblies are not necessarily linear, but instead are presented in the form of a graph. This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 23583: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23583: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23583: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/lucidrains\/alphafold2\" id=\"link-24137\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Alphafold2-Pytorch<\/a>\n<!-- Time to render name section of link id 24137: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An unofficial working Pytorch implementation of Alphafold2, a 3D protein predictor.<\/p>\n<!-- Time to render link large description section of link id 24137: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24137: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24137: 0.00017189979553223 --> \n<tr><td><a href=\"https:\/\/alphagenes.roslin.ed.ac.uk\/wp\/software\/alphaimpute\/\" id=\"link-24012\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlphaImpute<\/a>\n<!-- Time to render name section of link id 24012: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AlphaImpute is a software package for imputing and phasing genotype data in diploid populations with pedigree information.<\/p>\n<!-- Time to render link large description section of link id 24012: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24012: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24012: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/marekborowiec\/AMAS\" id=\"link-24138\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AMAS<\/a>\n<!-- Time to render name section of link id 24138: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Calculate summary statistics and manipulate multiple sequence alignments.<\/p>\n<!-- Time to render link large description section of link id 24138: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24138: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24138: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/amos\/\" id=\"link-23584\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AMOS<\/a>\n<!-- Time to render name section of link id 23584: 1.2874603271484E-5 --> \n<\/td>\n<td><p>A Modular, Open-Source whole genome assembler.<\/p>\n<!-- Time to render link large description section of link id 23584: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23584: 1.9073486328125E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23584: 0.00019598007202148 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/ampliconnoise\/\" id=\"link-23585\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ampliconnoise<\/a>\n<!-- Time to render name section of link id 23585: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal.<\/p>\n<!-- Time to render link large description section of link id 23585: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23585: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23585: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/sixthresearcher\/amplisat\" id=\"link-25403\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AmpliSAT<\/a>\n<!-- Time to render name section of link id 25403: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AmpliSAT (Amplicon Sequencing Analysis Tools) are a set of online tools that make easy the analysis of Amplicon Sequencing experiments.<\/p>\n<!-- Time to render link large description section of link id 25403: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AmpliSAT> How to use <\/a>\n<!-- Time to render notes section of link id 25403: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25403: 0.00016617774963379 --> \n<tr><td><a href=\"https:\/\/github.com\/hringbauer\/ancIBD\" id=\"link-25115\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ancIBD<\/a>\n<!-- Time to render name section of link id 25115: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Identify IBD segments between pairs of individuals in ancient human DNA data.<\/p>\r\n<p>The software package\u00a0<code class=\"docutils literal notranslate\"><span class=\"pre\">ancIBD<\/span><\/code>\u00a0detects Identity-by-Descent (IBD) segments in typical human aDNA data, implementing an algorithm described\u00a0<a class=\"reference external\" href=\"https:\/\/doi.org\/10.1101\/2023.03.08.531671\">in this preprint<\/a>. The input data are imputed and phased genotype data. The default parameters of\u00a0<code class=\"docutils literal notranslate\"><span class=\"pre\">ancIBD<\/span><\/code>\u00a0are optimized for imputed data using the software\u00a0<a class=\"reference external\" href=\"https:\/\/odelaneau.github.io\/GLIMPSE\/glimpse1\/index.html\">GLIMPSE<\/a>\u00a0using the 1000 Genome haplotype reference panel.<\/p>\r\n<p>Software documentation <a href=\"https:\/\/ancibd.readthedocs.io\/en\/latest\/\">here<\/a>.<\/p>\n<!-- Time to render link large description section of link id 25115: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ancIBD> How to use <\/a>\n<!-- Time to render notes section of link id 25115: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25115: 0.0001680850982666 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/ANGEL\" id=\"link-24007\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ANGEL<\/a>\n<!-- Time to render name section of link id 24007: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Robust Open Reading Frame prediction (ANGLE re-implementation)<\/p>\n<!-- Time to render link large description section of link id 24007: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24007: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24007: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/www.popgen.dk\/angsd\/index.php\/Main_Page#Overview\" id=\"link-23586\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ANGSD<\/a>\n<!-- Time to render name section of link id 23586: 3.814697265625E-6 --> \n<\/td>\n<td><p>ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities.<\/p>\n<!-- Time to render link large description section of link id 23586: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ANGSD> How to use <\/a>\n<!-- Time to render notes section of link id 23586: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23586: 0.00016617774963379 --> \n<tr><td><a href=\"https:\/\/lbgi.fr\/AnnotSV\/\" id=\"link-25353\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AnnotSV<\/a>\n<!-- Time to render name section of link id 25353: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An integrated tool for Structural Variations annotation and ranking.<\/p>\n<!-- Time to render link large description section of link id 25353: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AnnotSV> How to use <\/a>\n<!-- Time to render notes section of link id 25353: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25353: 0.00016593933105469 --> \n<tr><td><a href=\"http:\/\/annovar.openbioinformatics.org\/en\/latest\/\" id=\"link-23818\" class=\"track_this_link \" rel=\"noopener noreferrer\">ANNOVAR<\/a>\n<!-- Time to render name section of link id 23818: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)<\/p>\n<!-- Time to render link large description section of link id 23818: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23818: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23818: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/anvio.org\/\" id=\"link-23858\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Anvio<\/a>\n<!-- Time to render name section of link id 23858: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Anvi\u2019o is an analysis and visualization platform for \u2018omics data. It brings together many aspects of today\u2019s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs.<\/p>\n<!-- Time to render link large description section of link id 23858: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Anvio> How to use <\/a>\n<!-- Time to render notes section of link id 23858: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23858: 0.00020599365234375 --> \n<tr><td><a href=\"http:\/\/apoplastp.csiro.au\/index.html\" id=\"link-23903\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ApoplastP<\/a>\n<!-- Time to render name section of link id 23903: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ApoplastP is a machine learning method for predicting localization of proteins to the plant apoplast. ApoplastP can distinguish non-apoplastic proteins from apoplastic proteins for both plant proteins and pathogen proteins. In particular, ApoplastP can predict if an effector localizes to the plant apoplast.<\/p>\n<!-- Time to render link large description section of link id 23903: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ApoplastP> How to use <\/a>\n<!-- Time to render notes section of link id 23903: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23903: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/apptainer\/apptainer\" id=\"link-25160\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Apptainer<\/a>\n<!-- Time to render name section of link id 25160: 3.0994415283203E-6 --> \n<\/td>\n<td>Apptainer is an open source container platform designed to be simple, fast, and secure.\n<!-- Time to render link large description section of link id 25160: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Apptainer> How to use <\/a>\n<!-- Time to render notes section of link id 25160: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25160: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/DominikBuchner\/apscale\" id=\"link-25174\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Apscale<\/a>\n<!-- Time to render name section of link id 25174: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data<\/p>\n<!-- Time to render link large description section of link id 25174: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Apscale> How to use <\/a>\n<!-- Time to render notes section of link id 25174: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25174: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/maiziex\/Aquila\" id=\"link-24139\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Aquila<\/a>\n<!-- Time to render name section of link id 24139: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Diploid personal genome assembly and comprehensive variant detection based on linked-reads.<\/p>\n<!-- Time to render link large description section of link id 24139: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24139: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24139: 0.00017809867858887 --> \n<tr><td><a href=\"http:\/\/mbio-serv2.mbioekol.lu.se\/ARAGORN\/\" id=\"link-23587\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARAGORN<\/a>\n<!-- Time to render name section of link id 23587: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ARAGORN is a program to detect tRNA genes and tmRNA genes in nucleotide sequence<\/p>\n<!-- Time to render link large description section of link id 23587: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23587: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23587: 0.00017881393432617 --> \n<tr><td><a href=\"https:\/\/github.com\/markhilt\/ARBitR\" id=\"link-24140\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARBitR<\/a>\n<!-- Time to render name section of link id 24140: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ARBitR is an overlap aware genome assembly scaffolder for linked sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24140: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24140: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24140: 0.00018095970153809 --> \n<tr><td><a href=\"http:\/\/ibest.github.io\/ARC\/\" id=\"link-24141\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARC<\/a>\n<!-- Time to render name section of link id 24141: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: - Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together. - Reducing\/removing reference bias as compared to mapping based approaches.<\/p>\n<!-- Time to render link large description section of link id 24141: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24141: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24141: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/arcs\/tree\/binomialx2\" id=\"link-23827\" class=\"track_this_link \" rel=\"noopener noreferrer\">ARCS<\/a>\n<!-- Time to render name section of link id 23827: 7.8678131103516E-6 --> \n<\/td>\n<td><p>Scaffolding genome sequence assemblies using 10X Genomics GemCode\/Chromium data<\/p>\n<!-- Time to render link large description section of link id 23827: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23827: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23827: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/CshlSiepelLab\/argweaver\/\" id=\"link-26136\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARGweaver<\/a>\n<!-- Time to render name section of link id 26136: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The ARGweaver\/ARGweaver-D software package contains programs and libraries for sampling and manipulating ancestral recombination graphs (ARGs).<\/p>\n<!-- Time to render link large description section of link id 26136: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ARGweaver> How to use <\/a>\n<!-- Time to render notes section of link id 26136: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26136: 0.00017881393432617 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/arks\" id=\"link-24005\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARKS<\/a>\n<!-- Time to render name section of link id 24005: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Scaffolding genome sequence assemblies using 10X Genomics GemCode\/Chromium data. This project is a new kmer-based (alignment free) implementation of ARCS. It provides improved runtime performance over the original ARCS implementation by removing the requirement to perform alignments with bwa mem.<\/p>\n<!-- Time to render link large description section of link id 24005: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24005: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24005: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/kingsfordgroup\/armatus\" id=\"link-24142\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Armatus<\/a>\n<!-- Time to render name section of link id 24142: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Multiresolution domain calling software for chromosome conformation capture interaction matrices. Armatus is a Topologically Associated Domain caller. Follow the Web page to know more about Armatus.<\/p>\n<!-- Time to render link large description section of link id 24142: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24142: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24142: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/suhrig\/arriba\" id=\"link-24143\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Arriba<\/a>\n<!-- Time to render name section of link id 24143: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 24143: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Arriba> How to use <\/a>\n<!-- Time to render notes section of link id 24143: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24143: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/skoren\/ArrowGrid\" id=\"link-24144\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ArrowGrid<\/a>\n<!-- Time to render name section of link id 24144: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The distribution is a parallel wrapper around the Arrow consensus framework within the SMRT Analysis Software<\/p>\n<!-- Time to render link large description section of link id 24144: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ArrowGrid> How to use <\/a>\n<!-- Time to render notes section of link id 24144: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24144: 0.0001981258392334 --> \n<tr><td><a href=\"https:\/\/www.niehs.nih.gov\/research\/resources\/software\/biostatistics\/art\/\" id=\"link-23928\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ART<\/a>\n<!-- Time to render name section of link id 23928: 2.8610229492188E-6 --> \n<\/td>\n<td><p>ART is a set of simulation tools to generate synthetic next-generation sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 23928: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23928: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23928: 0.00018715858459473 --> \n<tr><td><a href=\"https:\/\/github.com\/YU-Zhejian\/art_modern\" id=\"link-26188\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">art_modern<\/a>\n<!-- Time to render name section of link id 26188: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A modern re-implementation of the popular ART simulator with enhanced performance and functionality.<\/p>\n<!-- Time to render link large description section of link id 26188: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_art_modern> How to use <\/a>\n<!-- Time to render notes section of link id 26188: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26188: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/delehef\/asgart\" id=\"link-24105\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASGART<\/a>\n<!-- Time to render name section of link id 24105: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ASGART (A Segmental duplications Gathering and Refinement Tool) is a multiplatform (GNU\/Linux, macOS, Windows) tool designed to search for large duplications amongst one or two DNA strands.<\/p>\n<!-- Time to render link large description section of link id 24105: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24105: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24105: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/BBaloglu\/ASHURE\" id=\"link-24145\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASHURE<\/a>\n<!-- Time to render name section of link id 24145: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Python-based pipeline for analyzing Nanopore sequencing metabarcoding data. ASHURE can take a reference database in order to improve accuracy.<\/p>\n<!-- Time to render link large description section of link id 24145: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24145: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24145: 0.00019598007202148 --> \n<tr><td><a href=\"https:\/\/github.com\/PalamaraLab\/ASMC\" id=\"link-24750\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASMC<\/a>\n<!-- Time to render name section of link id 24750: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Ascertained Sequentially Markovian Coalescent (contains ASMC and an extension, FastSMC, together with python bindings for both)<\/p>\n<!-- Time to render link large description section of link id 24750: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ASMC> How to use <\/a>\n<!-- Time to render notes section of link id 24750: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24750: 0.00017881393432617 --> \n<tr><td><a href=\"https:\/\/github.com\/ucdavis-bioinformatics\/assemblathon2-analysis\" id=\"link-25078\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">assemblathon2<\/a>\n<!-- Time to render name section of link id 25078: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This repo contains a motley assortment of unpublished scripts and commands used by Ian Korf, Keith Bradnam, and Joe Fass in the analysis of Assemblathon 2 competition entries (assemblies).<\/p>\n<!-- Time to render link large description section of link id 25078: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_assemblathon2> How to use <\/a>\n<!-- Time to render notes section of link id 25078: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25078: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-pathogens\/assembly-stats\" id=\"link-23972\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">assembly-stats<\/a>\n<!-- Time to render name section of link id 23972: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Get assembly statistics from FASTA and FASTQ files.<\/p>\n<!-- Time to render link large description section of link id 23972: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23972: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23972: 0.0001838207244873 --> \n<tr><td><a href=\"https:\/\/github.com\/marianattestad\/assemblytics\" id=\"link-24999\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Assemblytics<\/a>\n<!-- Time to render name section of link id 24999: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24999: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24999: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24999: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/yhadevol\/Assexon\" id=\"link-24146\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Assexon<\/a>\n<!-- Time to render name section of link id 24146: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assembling Exon Using Gene Capture Data<\/p>\n<!-- Time to render link large description section of link id 24146: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24146: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24146: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/chaoszhang\/ASTER\" id=\"link-24147\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASTER<\/a>\n<!-- Time to render name section of link id 24147: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A family of ASTRAL-like algorithms.<\/p>\n<!-- Time to render link large description section of link id 24147: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ASTER> How to use <\/a>\n<!-- Time to render notes section of link id 24147: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24147: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/smirarab\/ASTRAL\" id=\"link-23901\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASTRAL<\/a>\n<!-- Time to render name section of link id 23901: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.<\/p>\n<!-- Time to render link large description section of link id 23901: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ASTRAL> How to use <\/a>\n<!-- Time to render notes section of link id 23901: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23901: 0.00018119812011719 --> \n<tr><td><a href=\"https:\/\/github.com\/chaoszhang\/A-pro\" id=\"link-24148\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASTRAL-Pro<\/a>\n<!-- Time to render name section of link id 24148: 1.1920928955078E-5 --> \n<\/td>\n<td><p>ASTRAL-Pro stands for ASTRAL for PaRalogs and Orthologs. ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.<\/p>\n<!-- Time to render link large description section of link id 24148: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24148: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24148: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/kundajelab\/atac_dnase_pipelines\" id=\"link-23874\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">atac dnase pipelines<\/a>\n<!-- Time to render name section of link id 23874: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ATAC-seq and DNase-seq processing pipeline. This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data.<\/p>\n<!-- Time to render link large description section of link id 23874: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23874: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23874: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/jdidion\/atropos\" id=\"link-23969\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Atropos<\/a>\n<!-- Time to render name section of link id 23969: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of Cutadapt read trimmer.<\/p>\n<!-- Time to render link large description section of link id 23969: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23969: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23969: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/sjdv1982\/attract\" id=\"link-25705\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ATTRACT<\/a>\n<!-- Time to render name section of link id 25705: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ATTRACT program suite for macromolecular docking (protein-protein, protein-nucleic acid, protein-peptide).<\/p>\n<!-- Time to render link large description section of link id 25705: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ATTRACT> How to use <\/a>\n<!-- Time to render notes section of link id 25705: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25705: 0.00018596649169922 --> \n<tr><td><a href=\"http:\/\/bioinf.uni-greifswald.de\/augustus\/\" id=\"link-23588\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Augustus<\/a>\n<!-- Time to render name section of link id 23588: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Augustus is a program that predicts genes in eukaryotic genomic sequences<\/p>\n<!-- Time to render link large description section of link id 23588: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Augustus> How to use <\/a>\n<!-- Time to render notes section of link id 23588: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23588: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/Jwindler\/AutoHiC\" id=\"link-25028\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AutoHiC<\/a>\n<!-- Time to render name section of link id 25028: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AutoHiC is a deep learning tool that uses Hi-C data to support genome assembly. It can automatically correct errors during genome assembly and generate genomes at the chromosome level.<\/p>\n<!-- Time to render link large description section of link id 25028: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AutoHiC> How to use <\/a>\n<!-- Time to render notes section of link id 25028: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25028: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/GDKO\/AvP\" id=\"link-24708\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AvP<\/a>\n<!-- Time to render name section of link id 24708: 2.1457672119141E-6 --> \n<\/td>\n<td><p>AvP performs automatic detection of HGT candidates within a phylogenetic framework.<\/p>\n<!-- Time to render link large description section of link id 24708: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AvP> How to use <\/a>\n<!-- Time to render notes section of link id 24708: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24708: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/docs.aws.amazon.com\/fr_fr\/cli\/latest\/userguide\/getting-started-install.html\" id=\"link-25023\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">awscli<\/a>\n<!-- Time to render name section of link id 25023: 2.1457672119141E-6 --> \n<\/td>\n<td>The AWS Command Line Interface (AWS CLI) is an open source tool that enables you to interact with AWS services using commands in your command-line shell.\n<!-- Time to render link large description section of link id 25023: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_aws> How to use <\/a>\n<!-- Time to render notes section of link id 25023: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25023: 0.00016593933105469 --> \n<tr><td><a href=\"https:\/\/github.com\/pierrepeterlongo\/back_to_sequences\" id=\"link-25269\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Back_to_sequences<\/a>\n<!-- Time to render name section of link id 25269: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Given a set of kmers (fasta \/ fastq <.gz> format) and a set of sequences (fasta \/ fastq <.gz> format), this tool will extract the sequences containing some of those kmers.<\/p>\n<!-- Time to render link large description section of link id 25269: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Back_to_sequences> How to use <\/a>\n<!-- Time to render notes section of link id 25269: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25269: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Badread\" id=\"link-26191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Badread<\/a>\n<!-- Time to render name section of link id 26191: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Badread is a long-read simulator tool that makes \u2013 you guessed it \u2013 bad reads! It can imitate many kinds of problems one might encounter in real long-read sets: chimeras, low-quality regions, systematic basecalling errors and more.<\/p>\n<!-- Time to render link large description section of link id 26191: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Badread> How to use <\/a>\n<!-- Time to render notes section of link id 26191: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26191: 0.00018620491027832 --> \n<tr><td><a href=\"http:\/\/bali-phy.org\" id=\"link-23974\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BAli-Phy<\/a>\n<!-- Time to render name section of link id 23974: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BAli-Phy is software by Ben Redelings that estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. It uses likelihood-based evolutionary models of substitutions and insertions and deletions to place gaps.<\/p>\n<!-- Time to render link large description section of link id 23974: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23974: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23974: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/willros\/bam2plot\" id=\"link-25605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bam2plot<\/a>\n<!-- Time to render name section of link id 25605: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Make coverage plots from bam files.<\/p>\n<!-- Time to render link large description section of link id 25605: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bam2plot> How to use <\/a>\n<!-- Time to render notes section of link id 25605: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25605: 0.0001680850982666 --> \n<tr><td><a href=\"https:\/\/udall-lab.byu.edu\/Research\/Software\/BamBam.aspx\" id=\"link-23922\" class=\"track_this_link \" rel=\"noopener noreferrer\">BamBam<\/a>\n<!-- Time to render name section of link id 23922: 1.9073486328125E-6 --> \n<\/td>\n<td><p>several simple-to-use tools to facilitate NGS analysis<\/p>\n<!-- Time to render link large description section of link id 23922: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23922: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23922: 0.00016093254089355 --> \n<tr><td><a href=\"https:\/\/github.com\/macroevolution\/bamm\" id=\"link-23913\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BAMM<\/a>\n<!-- Time to render name section of link id 23913: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A program for multimodel inference on speciation and trait evolution.<\/p>\n<!-- Time to render link large description section of link id 23913: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23913: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23913: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/laneatmore\/BAMscorer\" id=\"link-24745\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BAMscorer<\/a>\n<!-- Time to render name section of link id 24745: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BAMscorer can be used to conduct genomic assignment tests from BAM files. Assignments can be done on genomic regions, inversions, and whole-genome datasets.<\/p>\n<!-- Time to render link large description section of link id 24745: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24745: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24745: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/guigolab\/bamstats\" id=\"link-24153\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bamstats (notsame as BAMstats)<\/a>\n<!-- Time to render name section of link id 24153: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bamstats is a command line tool written in Go for computing mapping statistics from a BAM file.<\/p>\n<!-- Time to render link large description section of link id 24153: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24153: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24153: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/10XGenomics\/bamtofastq\" id=\"link-24154\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bamtofastq<\/a>\n<!-- Time to render name section of link id 24154: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files.<\/p>\n<!-- Time to render link large description section of link id 24154: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bamtofastq> How to use <\/a>\n<!-- Time to render notes section of link id 24154: 1.0967254638672E-5 --> \n<\/td><\/tr>\n<!-- Time to render link id 24154: 0.00019121170043945 --> \n<tr><td><a href=\"https:\/\/github.com\/pezmaster31\/bamtools\" id=\"link-23589\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bamtools<\/a>\n<!-- Time to render name section of link id 23589: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.<\/p>\n<!-- Time to render link large description section of link id 23589: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bamtools> How to use <\/a>\n<!-- Time to render notes section of link id 23589: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23589: 0.00018215179443359 --> \n<tr><td><a href=\"http:\/\/genome.sph.umich.edu\/wiki\/BamUtil\" id=\"link-23590\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bamUtil<\/a>\n<!-- Time to render name section of link id 23590: 2.8610229492188E-6 --> \n<\/td>\n<td><p>bamUtil is a repository that contains several programs that perform operations on SAM\/BAM files. All of these programs are built into a single executable, bam.<\/p>\n<!-- Time to render link large description section of link id 23590: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bamUtil> How to use <\/a>\n<!-- Time to render notes section of link id 23590: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23590: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/asl\/BandageNG\" id=\"link-25521\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bandage-NG<\/a>\n<!-- Time to render name section of link id 25521: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bandage-NG is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as SPAdes, MEGAHIT and others.<\/p>\n<!-- Time to render link large description section of link id 25521: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bandage-NG> How to use <\/a>\n<!-- Time to render notes section of link id 25521: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25521: 0.00016403198242188 --> \n<tr><td><a href=\"http:\/\/www.vicbioinformatics.com\/software.shtml\" id=\"link-23591\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Barrnap<\/a>\n<!-- Time to render name section of link id 23591: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).<\/p>\n<!-- Time to render link large description section of link id 23591: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23591: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23591: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/github.com\/stevemussmann\/BayesAss3-SNPs\" id=\"link-24155\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayesAss3-SNPs<\/a>\n<!-- Time to render name section of link id 24155: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Modification of BayesAss 3.0.4 to allow handling of large SNP datasets.<\/p>\n<!-- Time to render link large description section of link id 24155: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BayesAss3-SNPs> How to use <\/a>\n<!-- Time to render notes section of link id 24155: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24155: 0.00017094612121582 --> \n<tr><td><a href=\"http:\/\/cmpg.unibe.ch\/software\/bayescan\/\" id=\"link-23592\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayeScan<\/a>\n<!-- Time to render name section of link id 23592: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Detecting natural selection from population-bases genetic data using differences in alleles frequencies between populations.<\/p>\n<!-- Time to render link large description section of link id 23592: 1.3113021850586E-5 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BayeScan> How to use <\/a>\n<!-- Time to render notes section of link id 23592: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23592: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/devillemereuil\/bayescenv\" id=\"link-23963\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayeScEnv<\/a>\n<!-- Time to render name section of link id 23963: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.<\/p>\n<!-- Time to render link large description section of link id 23963: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23963: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23963: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/www.evolution.rdg.ac.uk\/BayesTraitsV3.0.1\/BayesTraitsV3.0.1.html\" id=\"link-24121\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayesTraits<\/a>\n<!-- Time to render name section of link id 24121: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.<\/p>\n<!-- Time to render link large description section of link id 24121: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24121: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24121: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/www1.montpellier.inra.fr\/CBGP\/software\/baypass\/\" id=\"link-23773\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayPass<\/a>\n<!-- Time to render name section of link id 23773: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and\/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).<\/p>\n<!-- Time to render link large description section of link id 23773: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BayPass> How to use <\/a>\n<!-- Time to render notes section of link id 23773: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23773: 0.00020599365234375 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/bbmap\/\" id=\"link-23785\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BBMap<\/a>\n<!-- Time to render name section of link id 23785: 1.9073486328125E-6 --> \n<\/td>\n<td><p>a short read aligner, as well as various other bioinformatic tools.<\/p>\n<!-- Time to render link large description section of link id 23785: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BBMap> How to use <\/a>\n<!-- Time to render notes section of link id 23785: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23785: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/GATB\/bcalm\" id=\"link-24156\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BCALM2<\/a>\n<!-- Time to render name section of link id 24156: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24156: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24156: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24156: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/samtools.github.io\/bcftools\/\" id=\"link-23880\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BCFtools<\/a>\n<!-- Time to render name section of link id 23880: 1.9073486328125E-6 --> \n<\/td>\n<td><p>utilities for variant calling and manipulating VCFs and BCFs.<\/p>\n<!-- Time to render link large description section of link id 23880: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bcftools> How to use <\/a>\n<!-- Time to render notes section of link id 23880: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23880: 0.00019502639770508 --> \n<tr><td><a href=\"http:\/\/support.illumina.com\/sequencing\/sequencing_software\/bcl2fastq-conversion-software.html\" id=\"link-23593\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bcl2fastq<\/a>\n<!-- Time to render name section of link id 23593: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The Bcl2FastQ conversion software is a new tool to handle bcl conversion and demultiplexing of both unzipped and zipped bcl files, which have reduced footprint and were introduced as an optional output of the HCS Software version 2.0<\/p>\n<!-- Time to render link large description section of link id 23593: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bcl2fastq> How to use <\/a>\n<!-- Time to render notes section of link id 23593: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23593: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/Malfoy\/BCOOL\" id=\"link-24157\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BCOOL<\/a>\n<!-- Time to render name section of link id 24157: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BCOOL is a read corrector for NGS sequencing data that align reads on a de Bruijn graph.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24157: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24157: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24157: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/faculty.washington.edu\/browning\/beagle\/beagle.html\" id=\"link-23594\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle<\/a>\n<!-- Time to render name section of link id 23594: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.<\/p>\n<!-- Time to render link large description section of link id 23594: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Beagle> How to use <\/a>\n<!-- Time to render notes section of link id 23594: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23594: 0.00018692016601562 --> \n<tr><td><a href=\"http:\/\/faculty.washington.edu\/browning\/beagle_utilities\/utilities.html\" id=\"link-24987\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle_Utilities<\/a>\n<!-- Time to render name section of link id 24987: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Simple utility programs for manipulating text files, especially VCF files.<\/p>\n<!-- Time to render link large description section of link id 24987: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24987: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24987: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/beagle-dev\/beagle-lib\" id=\"link-24016\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle-lib<\/a>\n<!-- Time to render name section of link id 24016: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BEAGLE-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages<\/p>\n<!-- Time to render link large description section of link id 24016: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Beagle-lib> How to use <\/a>\n<!-- Time to render notes section of link id 24016: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24016: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/beast.community\" id=\"link-24130\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BEAST<\/a>\n<!-- Time to render name section of link id 24130: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.<\/p>\r\n<p>BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.<\/p>\n<!-- Time to render link large description section of link id 24130: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BEAST> How to use <\/a>\n<!-- Time to render notes section of link id 24130: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24130: 0.00020480155944824 --> \n<tr><td><a href=\"http:\/\/beast2.org\/\" id=\"link-23805\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BEAST2<\/a>\n<!-- Time to render name section of link id 23805: 7.8678131103516E-6 --> \n<\/td>\n<td><p>BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.<\/p>\n<!-- Time to render link large description section of link id 23805: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BEAST2> How to use <\/a>\n<!-- Time to render notes section of link id 23805: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23805: 0.00061202049255371 --> \n<tr><td><a href=\"http:\/\/bedops.readthedocs.io\/en\/latest\/index.html\" id=\"link-23865\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BEDOPS<\/a>\n<!-- Time to render name section of link id 23865: 8.1062316894531E-6 --> \n<\/td>\n<td><p>BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.<\/p>\n<!-- Time to render link large description section of link id 23865: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BEDOPS> How to use <\/a>\n<!-- Time to render notes section of link id 23865: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23865: 0.0005190372467041 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/bedtools\/\" id=\"link-23595\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bedtools<\/a>\n<!-- Time to render name section of link id 23595: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.<\/p>\n<!-- Time to render link large description section of link id 23595: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bedtools> How to use <\/a>\n<!-- Time to render notes section of link id 23595: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23595: 0.00047397613525391 --> \n<tr><td><a href=\"https:\/\/github.com\/giuliaguidi\/bella\" id=\"link-24108\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BELLA<\/a>\n<!-- Time to render name section of link id 24108: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A computationally-efficient and highly-accurate long-read to long-read aligner and overlapper.<\/p>\n<!-- Time to render link large description section of link id 24108: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24108: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24108: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/wegmannlab\/bexy\/src\/master\/\" id=\"link-25588\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BeXY<\/a>\n<!-- Time to render name section of link id 25588: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BeXY is a tool to jointly infer sex karyotypes and sex-linked scaffolds from read count data. It can also be used to genetically sex single individuals. BeXY is a command-line tool, and we provide an easy-to-use R package to visualize and parse the results.<\/p>\n<!-- Time to render link large description section of link id 25588: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BeXY> How to use <\/a>\n<!-- Time to render notes section of link id 25588: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25588: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/bgcsoftware\/\" id=\"link-24159\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bgc<\/a>\n<!-- Time to render name section of link id 24159: 2.1457672119141E-6 --> \n<\/td>\n<td><p>bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci.<\/p>\n<!-- Time to render link large description section of link id 24159: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24159: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24159: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/pmelsted\/bifrost\" id=\"link-24997\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bifrost<\/a>\n<!-- Time to render name section of link id 24997: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Highly parallel construction and indexing of colored and compacted de Bruijn graphs.<\/p>\n<!-- Time to render link large description section of link id 24997: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bifrost> How to use <\/a>\n<!-- Time to render notes section of link id 24997: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24997: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/git.wageningenur.nl\/medema-group\/BiG-SCAPE\" id=\"link-24080\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BIG-SCAPE<\/a>\n<!-- Time to render name section of link id 24080: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Biosynthetic Genes Similarity Clustering and Prospecting Engine. Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency Index)<\/p>\n<!-- Time to render link large description section of link id 24080: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24080: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24080: 0.00018715858459473 --> \n<tr><td><a href=\"http:\/\/pcingola.github.com\/BigDataScript\/\" id=\"link-23934\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BigDataScript<\/a>\n<!-- Time to render name section of link id 23934: 2.0980834960938E-5 --> \n<\/td>\n<td><p>BigDataScript is intended as a scripting language for big data pipeline<\/p>\n<!-- Time to render link large description section of link id 23934: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23934: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23934: 0.00018477439880371 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/bioawk\" id=\"link-24687\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bioawk<\/a>\n<!-- Time to render name section of link id 24687: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA\/Q and TAB-delimited formats with column names.<\/p>\n<!-- Time to render link large description section of link id 24687: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bioawk> How to use <\/a>\n<!-- Time to render notes section of link id 24687: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24687: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/ustenzel\/biohazard-tools\/src\/master\/\" id=\"link-24113\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">biohazard-tools<\/a>\n<!-- Time to render name section of link id 24113: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This is a collection of command line utilities that do useful stuff involving BAM files for Next Generation Sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24113: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24113: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24113: 0.00016617774963379 --> \n<tr><td><a href=\"https:\/\/github.com\/maasha\/biopieces\" id=\"link-24160\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Biopieces<\/a>\n<!-- Time to render name section of link id 24160: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks.<\/p>\n<!-- Time to render link large description section of link id 24160: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24160: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24160: 0.00016379356384277 --> \n<tr><td><a href=\"http:\/\/biopython.org\/wiki\/Biopython\" id=\"link-23596\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BIOPYTHON<\/a>\n<!-- Time to render name section of link id 23596: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.<\/p>\n<!-- Time to render link large description section of link id 23596: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.11.1<br> (see &quot;search_Python_module&quot; script <br> to search in others Python versions)\n<!-- Time to render notes section of link id 23596: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23596: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/institut-de-genomique\/biscot\" id=\"link-24692\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BiSCoT<\/a>\n<!-- Time to render name section of link id 24692: 2.8610229492188E-6 --> \n<\/td>\n<td><p>BiSCoT is a tool that aims to improve the contiguity of scaffolds and contigs generated after a Bionano scaffolding.<\/p>\n<!-- Time to render link large description section of link id 24692: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24692: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24692: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/huishenlab.github.io\/biscuit\/\" id=\"link-25356\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BISCUIT<\/a>\n<!-- Time to render name section of link id 25356: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BISulfite-seq CUI Toolkit (BISCUIT) is a utility for analyzing sodium bisulfite conversion-based DNA methylation\/modification data.<\/p>\n<!-- Time to render link large description section of link id 25356: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BISCUIT> How to use <\/a>\n<!-- Time to render notes section of link id 25356: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25356: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/bismark\/\" id=\"link-23597\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bismark<\/a>\n<!-- Time to render name section of link id 23597: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool to map bisulfite converted sequence reads and determine cytosine methylation states<\/p>\n<!-- Time to render link large description section of link id 23597: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bismark> How to use <\/a>\n<!-- Time to render notes section of link id 23597: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23597: 0.00019717216491699 --> \n<tr><td><a href=\"https:\/\/github.com\/dnaase\/Bis-tools\" id=\"link-24161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BisSNP<\/a>\n<!-- Time to render name section of link id 24161: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Accurate combined SNP\/Methylation calling.<\/p>\n<!-- Time to render link large description section of link id 24161: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24161: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24161: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/DevNet\/wiki\/Compatible-Software\" id=\"link-23598\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Blasr<\/a>\n<!-- Time to render name section of link id 23598: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Reference-based alignment<\/p>\n<!-- Time to render link large description section of link id 23598: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> ( See SMRTLink) <\/a>\n<!-- Time to render notes section of link id 23598: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23598: 0.00018596649169922 --> \n<tr><td><a href=\"http:\/\/genome.ucsc.edu\/\" id=\"link-23599\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">blat<\/a>\n<!-- Time to render name section of link id 23599: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The BLAST-Like Alignment Tool: similarity search in databanks. BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.<\/p>\n<!-- Time to render link large description section of link id 23599: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_blat> How to use <\/a>\n<!-- Time to render notes section of link id 23599: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23599: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/shimlab\/BLAZE\" id=\"link-25811\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BLAZE<\/a>\n<!-- Time to render name section of link id 25811: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Barcode identification from Long reads for AnalyZing single-cell gene Expression. SingleCell Nanopore sequencing data analysis.<\/p>\n<!-- Time to render link large description section of link id 25811: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BLAZE> How to use <\/a>\n<!-- Time to render notes section of link id 25811: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25811: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/DRL\/blobtools\" id=\"link-24162\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BlobTools<\/a>\n<!-- Time to render name section of link id 24162: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.<\/p>\n<!-- Time to render link large description section of link id 24162: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BlobTools> How to use <\/a>\n<!-- Time to render notes section of link id 24162: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24162: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/pavanvidem\/blockclust\" id=\"link-24025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BlockClust<\/a>\n<!-- Time to render name section of link id 24025: 2.8610229492188E-6 --> \n<\/td>\n<td><p>BlockClust is an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. BlockClust allows both clustering and classification of small non-coding RNAs.<\/p>\n<!-- Time to render link large description section of link id 24025: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24025: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24025: 0.00019311904907227 --> \n<tr><td><a href=\"https:\/\/github.com\/Psy-Fer\/blue-crab\" id=\"link-25792\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">blue-crab<\/a>\n<!-- Time to render name section of link id 25792: 3.0994415283203E-6 --> \n<\/td>\n<td><p>blue-crab is a conversion tool to convert from ONT's POD5 format to the community maintained SLOW5\/BLOW5 format.<\/p>\n<!-- Time to render link large description section of link id 25792: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_blue-crab> How to use <\/a>\n<!-- Time to render notes section of link id 25792: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25792: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/DominikBuchner\/BOLDigger\" id=\"link-25005\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BOLDigger<\/a>\n<!-- Time to render name section of link id 25005: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Python program to query .fasta files against the different databases of www.boldsystems.org<\/p>\n<!-- Time to render link large description section of link id 25005: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BOLDigger> How to use <\/a>\n<!-- Time to render notes section of link id 25005: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25005: 0.00029778480529785 --> \n<tr><td><a href=\"https:\/\/github.com\/DominikBuchner\/BOLDigger2\" id=\"link-25523\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BOLDigger2<\/a>\n<!-- Time to render name section of link id 25523: 4.0531158447266E-6 --> \n<\/td>\n<td><p>An even better Python program to query .fasta files against the COI database of www.boldsystems.org<\/p>\n<!-- Time to render link large description section of link id 25523: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BOLDigger2> How to use <\/a>\n<!-- Time to render notes section of link id 25523: 2.9087066650391E-5 --> \n<\/td><\/tr>\n<!-- Time to render link id 25523: 0.00028586387634277 --> \n<tr><td><a href=\"https:\/\/alkesgroup.broadinstitute.org\/BOLT-LMM\" id=\"link-26186\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BOLT-LMM<\/a>\n<!-- Time to render name section of link id 26186: 4.0531158447266E-6 --> \n<\/td>\n<td><p>The BOLT-LMM software package consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).<\/p>\n<!-- Time to render link large description section of link id 26186: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BOLT-LMM> How to use <\/a>\n<!-- Time to render notes section of link id 26186: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26186: 0.00025606155395508 --> \n<tr><td><a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\" id=\"link-23600\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bowtie<\/a>\n<!-- Time to render name section of link id 23600: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).<\/p>\n<!-- Time to render link large description section of link id 23600: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bowtie> How to use <\/a>\n<!-- Time to render notes section of link id 23600: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23600: 0.00026106834411621 --> \n<tr><td><a href=\"http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/index.shtml\" id=\"link-23601\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bowtie2<\/a>\n<!-- Time to render name section of link id 23601: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.<\/p>\n<!-- Time to render link large description section of link id 23601: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bowtie> How to use <\/a>\n<!-- Time to render notes section of link id 23601: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23601: 0.0002601146697998 --> \n<tr><td><a href=\"https:\/\/github.com\/bpp\/bpp\" id=\"link-24163\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BPP<\/a>\n<!-- Time to render name section of link id 24163: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Bayesian analysis of genomic sequence data under the multispecies coalescent model.<\/p>\n<!-- Time to render link large description section of link id 24163: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24163: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24163: 0.00024914741516113 --> \n<tr><td><a href=\"https:\/\/github.com\/jenniferlu717\/Bracken\" id=\"link-23966\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bracken<\/a>\n<!-- Time to render name section of link id 23966: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.<\/p>\n<!-- Time to render link large description section of link id 23966: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bracken> How to use <\/a>\n<!-- Time to render notes section of link id 23966: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23966: 0.00025200843811035 --> \n<tr><td><a href=\"http:\/\/bioinf.uni-greifswald.de\/bioinf\/braker\/index.html\" id=\"link-23782\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Braker<\/a>\n<!-- Time to render name section of link id 23782: 6.9141387939453E-6 --> \n<\/td>\n<td><p>BRAKER(1,2,3) is a tool for fully automated genome annotation with GeneMark-ET and AUGUSTUS<\/p>\n<!-- Time to render link large description section of link id 23782: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BRAKER> How to use <\/a>\n<!-- Time to render notes section of link id 23782: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23782: 0.00056099891662598 --> \n<tr><td><a href=\"https:\/\/github.com\/genome\/breakdancer\" id=\"link-24036\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BreakDancer<\/a>\n<!-- Time to render name section of link id 24036: 7.8678131103516E-6 --> \n<\/td>\n<td><p>SV detection from paired end reads mapping.<\/p>\n<!-- Time to render link large description section of link id 24036: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BreakDancer> How to use <\/a>\n<!-- Time to render notes section of link id 24036: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24036: 0.00053191184997559 --> \n<tr><td><a href=\"http:\/\/barricklab.org\/twiki\/bin\/view\/Lab\/ToolsBacterialGenomeResequencing\" id=\"link-23812\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">breseq<\/a>\n<!-- Time to render name section of link id 23812: 7.1525573730469E-6 --> \n<\/td>\n<td><p>breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.<\/p>\n<!-- Time to render link large description section of link id 23812: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_breseq> How to use <\/a>\n<!-- Time to render notes section of link id 23812: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23812: 0.0005340576171875 --> \n<tr><td><a href=\"https:\/\/github.com\/fmaguire\/Bridger_Assembler\" id=\"link-24746\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bridger<\/a>\n<!-- Time to render name section of link id 24746: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Bridger is an efficient de novo trascriptome assembler for RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 24746: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bridger> How to use <\/a>\n<!-- Time to render notes section of link id 24746: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24746: 0.0005497932434082 --> \n<tr><td><a href=\"http:\/\/pellegrini-legacy.mcdb.ucla.edu\/bs_seeker2\/\" id=\"link-24165\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BS-Seeker2-<\/a>\n<!-- Time to render name section of link id 24165: 7.1525573730469E-6 --> \n<\/td>\n<td><p>BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.<\/p>\n<!-- Time to render link large description section of link id 24165: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24165: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24165: 0.00055193901062012 --> \n<tr><td><a href=\"https:\/\/github.com\/hellbelly\/BS-Snper\" id=\"link-24166\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BS-SNPer<\/a>\n<!-- Time to render name section of link id 24166: 6.9141387939453E-6 --> \n<\/td>\n<td><p>BS-SNPer is an ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM\/SAM format using approximate Bayesian modeling.<\/p>\n<!-- Time to render link large description section of link id 24166: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24166: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24166: 0.00050902366638184 --> \n<tr><td><a href=\"https:\/\/code.google.com\/p\/bsmap\/\" id=\"link-23602\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BSMAP<\/a>\n<!-- Time to render name section of link id 23602: 6.9141387939453E-6 --> \n<\/td>\n<td><p>BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference<\/p>\n<!-- Time to render link large description section of link id 23602: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23602: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23602: 0.00029110908508301 --> \n<tr><td><a href=\"http:\/\/graphics.med.yale.edu\/trim\/\" id=\"link-24125\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Btrim<\/a>\n<!-- Time to render name section of link id 24125: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A fast and accurate adapter, barcodes, and low-quality region trimming and binning program written in C for next-generating sequencing reads. The search algorithm is based on Eugene Myers' fast bit-vector algorithm.<\/p>\n<!-- Time to render link large description section of link id 24125: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24125: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24125: 0.00021505355834961 --> \n<tr><td><a href=\"http:\/\/www.stat.wisc.edu\/~ane\/bucky\/index.html\" id=\"link-23995\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BUCKy<\/a>\n<!-- Time to render name section of link id 23995: 2.8610229492188E-6 --> \n<\/td>\n<td><p>BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis.<\/p>\n<!-- Time to render link large description section of link id 23995: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23995: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23995: 0.00022482872009277 --> \n<tr><td><a href=\"http:\/\/busco.ezlab.org\/v2\/\" id=\"link-23844\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BUSCO<\/a>\n<!-- Time to render name section of link id 23844: 2.8610229492188E-6 --> \n<\/td>\n<td><p>BUSCO v2 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9. BUSCO assessments are implemented in open-source software, with a large selection of lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.<\/p>\n<!-- Time to render link large description section of link id 23844: 2.6941299438477E-5 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BUSCO> How to use <\/a>\n<!-- Time to render notes section of link id 23844: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23844: 0.0002439022064209 --> \n<tr><td><a href=\"https:\/\/github.com\/jamiemcg\/BUSCO_phylogenomics\" id=\"link-25092\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BUSCO_phylogenomics<\/a>\n<!-- Time to render name section of link id 25092: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This is a Python pipeline to construct species phylogenies using BUSCO proteins. It works directly from BUSCO output and can generate concatenated supermatrix alignments and also gene trees of BUSCO families.<\/p>\r\n<p dir=\"auto\">The pipeline identifies BUSCO proteins that are complete and single-copy in all input samples. Alternatively, you can account for missing data and choose to include BUSCO proteins that are complete and single-copy in a certain percentage of input samples. Each BUSCO family is individually aligned, trimmed, and then concatenated together to generate a supermatrix alignment. The pipeline also identifies BUSCO proteins that are complete and single-copy in at least 4 input samples, and generates gene trees for each of these families.<\/p>\n<!-- Time to render link large description section of link id 25092: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BUSCO_phylogenomics> How to use <\/a>\n<!-- Time to render notes section of link id 25092: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25092: 0.00021791458129883 --> \n<tr><td><a href=\"https:\/\/github.com\/lstevens17\/busco2fasta\" id=\"link-25024\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">busco2fasta<\/a>\n<!-- Time to render name section of link id 25024: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A script to turn a set of BUSCO results into a directory of multisequence FASTA files.<\/p>\n<!-- Time to render link large description section of link id 25024: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 25024: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25024: 0.00021100044250488 --> \n<tr><td><a href=\"https:\/\/github.com\/BUStools\/bustools\" id=\"link-24167\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bustools<\/a>\n<!-- Time to render name section of link id 24167: 3.0994415283203E-6 --> \n<\/td>\n<td><p>bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.<\/p>\n<!-- Time to render link large description section of link id 24167: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24167: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24167: 0.00021696090698242 --> \n<tr><td><a href=\"http:\/\/bio-bwa.sourceforge.net\/\" id=\"link-23603\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwa<\/a>\n<!-- Time to render name section of link id 23603: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.<\/p>\n<!-- Time to render link large description section of link id 23603: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bwa> How to use <\/a>\n<!-- Time to render notes section of link id 23603: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23603: 0.00022387504577637 --> \n<tr><td><a href=\"https:\/\/github.com\/bwa-mem2\/bwa-mem2\" id=\"link-24168\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwa-mem2<\/a>\n<!-- Time to render name section of link id 24168: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster.<\/p>\n<!-- Time to render link large description section of link id 24168: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bwa-mem2> How to use <\/a>\n<!-- Time to render notes section of link id 24168: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24168: 0.0002131462097168 --> \n<tr><td><a href=\"https:\/\/github.com\/brentp\/bwa-meth\" id=\"link-24169\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwa-meth<\/a>\n<!-- Time to render name section of link id 24169: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.<\/p>\n<!-- Time to render link large description section of link id 24169: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bwa-meth> How to use <\/a>\n<!-- Time to render notes section of link id 24169: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24169: 0.00022506713867188 --> \n<tr><td><a href=\"https:\/\/github.com\/CRG-Barcelona\/bwtool\/wiki\" id=\"link-23779\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwtools<\/a>\n<!-- Time to render name section of link id 23779: 2.8610229492188E-6 --> \n<\/td>\n<td><p>bwtool is a command-line utility for bigWig files.<\/p>\n<!-- Time to render link large description section of link id 23779: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23779: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23779: 0.00021505355834961 --> \n<tr><td><a href=\"https:\/\/www.haskell.org\/cabal\/\" id=\"link-24112\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cabal<\/a>\n<!-- Time to render name section of link id 24112: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Cabal is the standard package system for Haskell software. It helps people to configure, build and install Haskell software and to distribute it easily to other users and developers.<\/p>\n<!-- Time to render link large description section of link id 24112: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24112: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24112: 0.0003960132598877 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/cactus\" id=\"link-24984\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cactus<\/a>\n<!-- Time to render name section of link id 24984: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit.<\/p>\n<!-- Time to render link large description section of link id 24984: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cactus> How to use <\/a>\n<!-- Time to render notes section of link id 24984: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24984: 0.00053501129150391 --> \n<tr><td><a href=\"https:\/\/github.com\/hahnlab\/CAFE5\" id=\"link-24171\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAFE<\/a>\n<!-- Time to render name section of link id 24171: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Software for Computational Analysis of gene Family Evolution. The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences.<\/p>\n<!-- Time to render link large description section of link id 24171: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAFE> How to use <\/a>\n<!-- Time to render notes section of link id 24171: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24171: 0.00054502487182617 --> \n<tr><td><a href=\"https:\/\/github.com\/BioComputingUP\/CAID\" id=\"link-25271\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAID<\/a>\n<!-- Time to render name section of link id 25271: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The CAID software produces all outputs necessary for Critical Assessment of Intrinsic Disorder (CAID) edition, including baselines, references, metrics and plots, starting from predictions and a reference (see Data Availability section to know how to obtain this data).<\/p>\n<!-- Time to render link large description section of link id 25271: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAID> How to use <\/a>\n<!-- Time to render notes section of link id 25271: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25271: 0.0005030632019043 --> \n<tr><td><a href=\"https:\/\/github.com\/CAMI-challenge\/AMBER\" id=\"link-24671\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAMI-AMBER<\/a>\n<!-- Time to render name section of link id 24671: 6.9141387939453E-6 --> \n<\/td>\n<td><p>AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets.<\/p>\n<!-- Time to render link large description section of link id 24671: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24671: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24671: 0.00050687789916992 --> \n<tr><td><a href=\"https:\/\/github.com\/EBI-Metagenomics\/emg-viral-pipeline\" id=\"link-25569\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAMISIM<\/a>\n<!-- Time to render name section of link id 25569: 7.1525573730469E-6 --> \n<\/td>\n<td><p>CAMISIM is a software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets.<\/p>\n<!-- Time to render link large description section of link id 25569: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAMISIM> How to use <\/a\n<!-- Time to render notes section of link id 25569: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25569: 0.00053596496582031 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/canu\" id=\"link-23781\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">canu<\/a>\n<!-- Time to render name section of link id 23781: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A single molecule sequence assembler for genomes large and small.<\/p>\n<!-- Time to render link large description section of link id 23781: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Canu> How to use <\/a>\n<!-- Time to render notes section of link id 23781: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23781: 0.00052309036254883 --> \n<tr><td><a href=\"http:\/\/seq.cs.iastate.edu\/\" id=\"link-24054\" class=\"track_this_link \" rel=\"noopener noreferrer\">CAP3<\/a>\n<!-- Time to render name section of link id 24054: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A DNA Sequence Assembly Program<\/p>\n<!-- Time to render link large description section of link id 24054: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAP3> How to use <\/a>\n<!-- Time to render notes section of link id 24054: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24054: 0.00021004676818848 --> \n<tr><td><a href=\"https:\/\/github.com\/kamimrcht\/CARNAC-LR\" id=\"link-24000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CARNAC-LR<\/a>\n<!-- Time to render name section of link id 24000: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Clustering coefficient-based Acquisition of RNA Communities in Long Reads.<\/p>\n<!-- Time to render link large description section of link id 24000: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24000: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24000: 0.00023078918457031 --> \n<tr><td><a href=\"https:\/\/github.com\/LouisPwr\/CarpeDeam\" id=\"link-25707\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CarpeDeam<\/a>\n<!-- Time to render name section of link id 25707: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CarpeDeam is a damage-aware metagenome assembler for ancient metagenomic DNA datasets. It takes (merged) reads and a damage matrix as input and prooved to work best for heavily damaged datasets.<\/p>\n<!-- Time to render link large description section of link id 25707: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CarpeDeam> How to use <\/a>\n<!-- Time to render notes section of link id 25707: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25707: 0.00021195411682129 --> \n<tr><td><a href=\"http:\/\/www.inra.fr\/mia\/T\/CarthaGene\/\" id=\"link-23604\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Carthagene<\/a>\n<!-- Time to render name section of link id 23604: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CarthaGene is a genetic\/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. CarthaGene can handle data made up of several distinct populations which t may each be either F2 backcross, recombinant inbred lines, F2 t intercross, phase known outbreds and\/or radiated hybrids (haploid t and diploid data).<\/p>\n<!-- Time to render link large description section of link id 23604: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23604: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23604: 0.00021195411682129 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/Comparative-Annotation-Toolkit\" id=\"link-23985\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAT<\/a>\n<!-- Time to render name section of link id 23985: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This project aims to provide a straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen.<\/p>\n<!-- Time to render link large description section of link id 23985: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23985: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23985: 0.00020909309387207 --> \n<tr><td><a href=\"https:\/\/github.com\/vrmarcelino\/CCMetagen\" id=\"link-24115\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CCMetagen<\/a>\n<!-- Time to render name section of link id 24115: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CCMetagen processes sequence alignments produced with KMA, which implements the ConClave sorting scheme to achieve highly accurate read mappings. CCMetagen processes sequence alignments produced with KMA, which implements the ConClave sorting scheme to achieve highly accurate read mappings. CCMetagen produces ranked taxonomic results in user-friendly formats that are ready for publication or downstream statistical analyses.<\/p>\n<!-- Time to render link large description section of link id 24115: 0.00039196014404297 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24115: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24115: 0.00062799453735352 --> \n<tr><td><a href=\"http:\/\/ccl.cse.nd.edu\/software\/downloadfiles.php\" id=\"link-23892\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cctools<\/a>\n<!-- Time to render name section of link id 23892: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.<\/p>\n<!-- Time to render link large description section of link id 23892: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23892: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23892: 0.00021219253540039 --> \n<tr><td><a href=\"http:\/\/cd-hit.org\" id=\"link-23605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cd-hit<\/a>\n<!-- Time to render name section of link id 23605: 3.0994415283203E-6 --> \n<\/td>\n<td><p>CD-HIT stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative.<\/p>\n<!-- Time to render link large description section of link id 23605: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CD-HIT> How to use <\/a>\n<!-- Time to render notes section of link id 23605: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23605: 0.00022196769714355 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/cdbfasta\" id=\"link-24172\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cdbfasta<\/a>\n<!-- Time to render name section of link id 24172: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This is a brief introduction to a couple of platform independent file-based hashing tools (cdbfasta and cdbyank) that can be used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files.<\/p>\n<!-- Time to render link large description section of link id 24172: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cdbfasta> How to use <\/a>\n<!-- Time to render notes section of link id 24172: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24172: 0.00021195411682129 --> \n<tr><td><a href=\"https:\/\/github.com\/Magdoll\/cDNA_Cupcake\" id=\"link-23996\" class=\"track_this_link \" rel=\"noopener noreferrer\">cDNA_Cupcake<\/a>\n<!-- Time to render name section of link id 23996: 3.0994415283203E-6 --> \n<\/td>\n<td><p>cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23996: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Cogent module\n<!-- Time to render notes section of link id 23996: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23996: 0.00021004676818848 --> \n<tr><td><a href=\"http:\/\/korflab.ucdavis.edu\/datasets\/cegma\/\" id=\"link-23606\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CEGMA<\/a>\n<!-- Time to render name section of link id 23606: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.<\/p>\n<!-- Time to render link large description section of link id 23606: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CEGMA> How to use <\/a>\n<!-- Time to render notes section of link id 23606: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23606: 0.0002129077911377 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell\/software\/pipelines\/latest\/what-is-cell-ranger\" id=\"link-23838\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger<\/a>\n<!-- Time to render name section of link id 23838: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3\u2019 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.<\/p>\n<!-- Time to render link large description section of link id 23838: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRanger> How to use <\/a>\n<!-- Time to render notes section of link id 23838: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23838: 0.00021791458129883 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell-multiome-atac-gex\/software\/overview\/welcome\" id=\"link-24173\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger ARC<\/a>\n<!-- Time to render name section of link id 24173: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cell Ranger ARC's pipelines analyze sequencing data produced from Chromium Single Cell Multiome ATAC + Gene Expression.<\/p>\n<!-- Time to render link large description section of link id 24173: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRangerARC> How to use <\/a>\n<!-- Time to render notes section of link id 24173: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24173: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell-atac\/software\/pipelines\/latest\/what-is-cell-ranger-atac\" id=\"link-24059\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger ATAC<\/a>\n<!-- Time to render name section of link id 24059: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.<\/p>\n<!-- Time to render link large description section of link id 24059: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRangerATAC> How to use <\/a>\n<!-- Time to render notes section of link id 24059: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24059: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell-dna\/software\/pipelines\/latest\/what-is-cell-ranger-dna\" id=\"link-24058\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger DNA<\/a>\n<!-- Time to render name section of link id 24058: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells.<\/p>\n<!-- Time to render link large description section of link id 24058: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24058: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24058: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/single-cell-genetics\/cellsnp-lite\" id=\"link-25928\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cellsnp-lite<\/a>\n<!-- Time to render name section of link id 25928: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cellsnp-lite is a C\/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs.<\/p>\n<!-- Time to render link large description section of link id 25928: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cellsnp-lite> How to use <\/a>\n<!-- Time to render notes section of link id 25928: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25928: 0.00015687942504883 --> \n<tr><td><a href=\"http:\/\/www.girinst.org\/downloads\/software\/censor\/\" id=\"link-23853\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CENSOR<\/a>\n<!-- Time to render name section of link id 23853: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CENSOR compares and masks protein or nucleotide sequences.<\/p>\n<!-- Time to render link large description section of link id 23853: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CENSOR> How to use <\/a>\n<!-- Time to render notes section of link id 23853: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23853: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/ccb.jhu.edu\/software\/centrifuge\/index.shtml\" id=\"link-23871\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Centrifuge<\/a>\n<!-- Time to render name section of link id 23871: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Classifier for metagenomic sequences. Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers.<\/p>\n<!-- Time to render link large description section of link id 23871: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Centrifuge> How to use <\/a>\n<!-- Time to render notes section of link id 23871: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23871: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/github.com\/junhaiqi\/centroAnno\" id=\"link-25684\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">centroAnno<\/a>\n<!-- Time to render name section of link id 25684: 3.0994415283203E-6 --> \n<\/td>\n<td><p>centroAnno is a prior-independent tool for automatic and efficient centromere\/tendem repeat structural analysis across multiple species. centroAnno supports the analysis of repeat units and higher-order tandem repeat units (HORs) in genome\/assembly, centromere sequence, and single sequencing long read.<\/p>\n<!-- Time to render link large description section of link id 25684: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_centroAnno> How to use <\/a>\n<!-- Time to render notes section of link id 25684: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25684: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/cgmlstfinder\" id=\"link-24174\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cgMLSTFinder<\/a>\n<!-- Time to render name section of link id 24174: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Core genome Multi-Locus Sequence Typing cgMLSTFinder runs KMA <1> against a chosen core genome MLST (cgMLST) database and outputs the detected alleles in a matrix file.<\/p>\n<!-- Time to render link large description section of link id 24174: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24174: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24174: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/ecogenomics.github.io\/CheckM\/\" id=\"link-25097\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CheckM<\/a>\n<!-- Time to render name section of link id 25097: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.<\/p>\n<!-- Time to render link large description section of link id 25097: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CheckM> How to use <\/a>\n<!-- Time to render notes section of link id 25097: 2.598762512207E-5 --> \n<\/td><\/tr>\n<!-- Time to render link id 25097: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/github.com\/chklovski\/CheckM2\" id=\"link-25590\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CheckM2<\/a>\n<!-- Time to render name section of link id 25590: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assessing the quality of metagenome-derived genome bins using machine learning.<\/p>\n<!-- Time to render link large description section of link id 25590: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CheckM2> How to use <\/a>\n<!-- Time to render notes section of link id 25590: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25590: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/comprna\/CHEUI\" id=\"link-25065\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CHEUI<\/a>\n<!-- Time to render name section of link id 25065: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CHEUI (Methylation (CH<sub>3<\/sub>) Estimation Using Ionic current) is an RNA modification detection software for Oxford Nanopore direct RNA sequencing data. CHEUI can be used to detect m6A and m5C in individual reads at single-nucleotide resolution from any sample (e.g. single condition), or detect differential m6A or m5C between any two conditions. CHEUI uses a two-stage deep learning method to detect m6A and m5C transcriptome-wide at single-read and single-site resolution in any sequence context (i.e. without any sequence constrains).<\/p>\n<!-- Time to render link large description section of link id 25065: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CHEUI> How to use <\/a>\n<!-- Time to render notes section of link id 25065: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25065: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/B-UMMI\/chewBBACA\" id=\"link-26081\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chewBBACA<\/a>\n<!-- Time to render name section of link id 26081: 3.0994415283203E-6 --> \n<\/td>\n<td><p><strong>chewBBACA<\/strong>\u00a0is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg\/wgMLST) schemas and results. The \"BBACA\" stands for \"BSR-Based Allele Calling Algorithm\". BSR stands for BLAST Score Ratio as proposed by\u00a0<a href=\"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-2\" rel=\"nofollow\">Rasko DA et al.<\/a>. The \"chew\" part adds extra coolness to the name and could be thought of as \"Comprehensive and Highly Efficient Workflow\".<\/p>\n<!-- Time to render link large description section of link id 26081: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chewBBACA> How to use <\/a>\n<!-- Time to render notes section of link id 26081: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26081: 0.00019311904907227 --> \n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/chimerascan\" id=\"link-24176\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chimerascan<\/a>\n<!-- Time to render name section of link id 24176: 1.9073486328125E-6 --> \n<\/td>\n<td><p>chimerascan is a software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.<\/p>\n<!-- Time to render link large description section of link id 24176: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24176: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24176: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/Chimera-tools\/ChimPipe\" id=\"link-23891\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ChimPipe<\/a>\n<!-- Time to render name section of link id 23891: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution.<\/p>\n<!-- Time to render link large description section of link id 23891: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23891: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23891: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/chopper\" id=\"link-25324\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chopper<\/a>\n<!-- Time to render name section of link id 25324: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.<\/p>\r\n<p>chopper is a tool that reunites the now outdated softwares NanoFilt and NanoLyse. It permits to filter QC files and has a faster execution time than NanoFilt and NanoLyse.<\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 25324: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chopper> How to use <\/a>\n<!-- Time to render notes section of link id 25324: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25324: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ChopStitch\" id=\"link-23931\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ChopStitch<\/a>\n<!-- Time to render name section of link id 23931: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23931: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23931: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23931: 0.00016593933105469 --> \n<tr><td><a href=\"https:\/\/github.com\/estebanpw\/chromeister\" id=\"link-24177\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chromeister<\/a>\n<!-- Time to render name section of link id 24177: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A dotplot generator for large chromosomes.<\/p>\n<!-- Time to render link large description section of link id 24177: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chromeister> How to use <\/a>\n<!-- Time to render notes section of link id 24177: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24177: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/catchenlab.life.illinois.edu\/chromonomer\/\" id=\"link-24178\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Chromonomer<\/a>\n<!-- Time to render name section of link id 24178: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Chromonomer is a program designed to integrate a genome assembly with a genetic map.<\/p>\n<!-- Time to render link large description section of link id 24178: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24178: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24178: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/koszullab\/chromosight\" id=\"link-25594\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Chromosight<\/a>\n<!-- Time to render name section of link id 25594: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Python package to detect chromatin loops (and other patterns) in Hi-C contact maps.<\/p>\n<!-- Time to render link large description section of link id 25594: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Chromosight> How to use <\/a>\n<!-- Time to render notes section of link id 25594: 3.0040740966797E-5 --> \n<\/td><\/tr>\n<!-- Time to render link id 25594: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/YangLab\/CIRCexplorer2\" id=\"link-25068\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CIRCexplorer2<\/a>\n<!-- Time to render name section of link id 25068: 2.1457672119141E-6 --> \n<\/td>\n<td><p>CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset<\/p>\n<!-- Time to render link large description section of link id 25068: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CIRCexplorer2> How to use <\/a>\n<!-- Time to render notes section of link id 25068: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25068: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/yangence\/circfull\" id=\"link-25401\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">circfull<\/a>\n<!-- Time to render name section of link id 25401: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool to detect and quantify full-length circRNA isoforms from circFL-seq.<\/p>\n<!-- Time to render link large description section of link id 25401: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_circfull> How to use <\/a>\n<!-- Time to render notes section of link id 25401: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25401: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/sanger-pathogens.github.io\/circlator\/\" id=\"link-23802\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Circlator<\/a>\n<!-- Time to render name section of link id 23802: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool to circularize genome assemblies<\/p>\n<!-- Time to render link large description section of link id 23802: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Circlator> How to use <\/a>\n<!-- Time to render notes section of link id 23802: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23802: 0.00016093254089355 --> \n<tr><td><a href=\"http:\/\/circos.ca\/\" id=\"link-23793\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">circos<\/a>\n<!-- Time to render name section of link id 23793: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Circos is a software package for visualizing data and information.<\/p>\n<!-- Time to render link large description section of link id 23793: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Circos> How to use <\/a>\n<!-- Time to render notes section of link id 23793: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23793: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/dieterich-lab\/circtools\" id=\"link-24117\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">circtools<\/a>\n<!-- Time to render name section of link id 24117: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.<\/p>\n<!-- Time to render link large description section of link id 24117: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24117: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24117: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/circuitscape.org\" id=\"link-25517\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Circuitscape<\/a>\n<!-- Time to render name section of link id 25517: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Circuitscape borrows algorithms from electronic circuit theory to predict patterns of movement, gene flow, and genetic differentiation among plant and animal populations in heterogeneous landscapes.<\/p>\n<!-- Time to render link large description section of link id 25517: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Circuitscape> How to use <\/a>\n<!-- Time to render notes section of link id 25517: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25517: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/ciri\" id=\"link-23911\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CIRI<\/a>\n<!-- Time to render name section of link id 23911: 2.1457672119141E-6 --> \n<\/td>\n<td><p>CIRI (circRNA identifier) is a novel chiastic clipping signal based algorithm, which can unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies.<\/p>\n<!-- Time to render link large description section of link id 23911: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23911: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23911: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfo-biols\/CIRI-long\" id=\"link-24179\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CIRI-long<\/a>\n<!-- Time to render name section of link id 24179: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Circular RNA Identification for Long-Reads Nanopore Sequencing Data.<\/p>\n<!-- Time to render link large description section of link id 24179: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CIRI-long> How to use <\/a>\n<!-- Time to render notes section of link id 24179: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24179: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/Hoohm\/CITE-seq-Count\" id=\"link-24180\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CITE-seq-Count<\/a>\n<!-- Time to render name section of link id 24180: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool that allows to get UMI counts from a single cell protein assay.<\/p>\n<!-- Time to render link large description section of link id 24180: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24180: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24180: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/HKU-BAL\/Clair3\" id=\"link-24181\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Clair3<\/a>\n<!-- Time to render name section of link id 24181: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.<\/p>\n<!-- Time to render link large description section of link id 24181: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Clair3> How to use <\/a>\n<!-- Time to render notes section of link id 24181: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24181: 0.00015592575073242 --> \n<tr><td><a href=\"https:\/\/github.com\/MikeAxtell\/CleaveLand4\" id=\"link-24110\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CleaveLand4<\/a>\n<!-- Time to render name section of link id 24110: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Analysis of degradome data to find sliced miRNA and siRNA targets<\/p>\n<!-- Time to render link large description section of link id 24110: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CleaveLand4> How to use <\/a>\n<!-- Time to render notes section of link id 24110: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24110: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/KCCG\/ClinSV\" id=\"link-25253\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClinSV<\/a>\n<!-- Time to render name section of link id 25253: 3.0994415283203E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25253: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClinSV> How to use <\/a>\n<!-- Time to render notes section of link id 25253: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25253: 0.00017189979553223 --> \n<tr><td><a href=\"https:\/\/github.com\/apeltzer\/ClipAndMerge\" id=\"link-24077\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClipAndMerge<\/a>\n<!-- Time to render name section of link id 24077: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Clip&amp;Merge is a tool to clip off adapters from sequencing reads and merge overlapping paired end reads together.<\/p>\n<!-- Time to render link large description section of link id 24077: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClipAndMerge> How to use <\/a>\n<!-- Time to render notes section of link id 24077: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24077: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/xavierdidelot\/ClonalFrameML\" id=\"link-25352\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClonalFrameML<\/a>\n<!-- Time to render name section of link id 25352: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A software package that performs efficient inference of recombination in bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 25352: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClonalFrameML> How to use <\/a>\n<!-- Time to render notes section of link id 25352: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25352: 0.00016403198242188 --> \n<tr><td><a href=\"http:\/\/clumpak.tau.ac.il\/\" id=\"link-23854\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CLUMPAK<\/a>\n<!-- Time to render name section of link id 23854: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Clustering Markov Packager Across K - was developed in order to aid users analyse the results of STRUCTURE-like programs. The software offers a few alternative modes of action, please go to the Help section for detailed about these modes.<\/p>\n<!-- Time to render link large description section of link id 23854: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CLUMPAK> How to use <\/a>\n<!-- Time to render notes section of link id 23854: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23854: 0.00016689300537109 --> \n<tr><td><a href=\"http:\/\/www.clustal.org\/omega\" id=\"link-23607\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Clustal Omega<\/a>\n<!-- Time to render name section of link id 23607: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks<\/p>\n<!-- Time to render link large description section of link id 23607: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClustalOmega> How to use <\/a>\n<!-- Time to render notes section of link id 23607: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23607: 0.00016307830810547 --> \n<tr><td><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/clustalw2\/index.html\" id=\"link-23608\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClustalW<\/a>\n<!-- Time to render name section of link id 23608: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Multiple sequence alignment program for DNA or proteins.<\/p>\n<!-- Time to render link large description section of link id 23608: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23608: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23608: 0.00020313262939453 --> \n<tr><td><a href=\"http:\/\/bio.cs.washington.edu\/yzizhen\/CMfinder\/\" id=\"link-24182\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CMfinder<\/a>\n<!-- Time to render name section of link id 24182: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CMfinder is a RNA motif prediction tool.<\/p>\n<!-- Time to render link large description section of link id 24182: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24182: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24182: 0.00016283988952637 --> \n<tr><td><a href=\"https:\/\/ftp.sanger.ac.uk\/pub\/resources\/software\/cnd\/\" id=\"link-25314\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cnD<\/a>\n<!-- Time to render name section of link id 25314: 2.1457672119141E-6 --> \n<\/td>\n<td><p>cnD is a program to detect copy number variants from short-read sequence data.<\/p>\n<!-- Time to render link large description section of link id 25314: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cnD> How to use <\/a>\n<!-- Time to render notes section of link id 25314: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25314: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/github.com\/etal\/cnvkit\" id=\"link-25090\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CNVkit<\/a>\n<!-- Time to render name section of link id 25090: 1.9073486328125E-6 --> \n<\/td>\n<td><p dir=\"auto\">A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.<\/p>\r\n<p dir=\"auto\">CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.<\/p>\r\n<p dir=\"auto\">Read the full documentation at:\u00a0<a href=\"http:\/\/cnvkit.readthedocs.io\/\" rel=\"nofollow\">http:\/\/cnvkit.readthedocs.io<\/a><\/p>\n<!-- Time to render link large description section of link id 25090: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CNVkit> How to use <\/a>\n<!-- Time to render notes section of link id 25090: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25090: 0.00016283988952637 --> \n<tr><td><a href=\"http:\/\/sv.gersteinlab.org\/\" id=\"link-23610\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CNVnator<\/a>\n<!-- Time to render name section of link id 23610: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool for CNV discovery and genotyping from depth of read mapping.<\/p>\n<!-- Time to render link large description section of link id 23610: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23610: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23610: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/genoweb.toulouse.inra.fr\/~fcabanettes\/cnv\/cnvpipelines_genotoul.pdf\" id=\"link-23946\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cnvpipelines<\/a>\n<!-- Time to render name section of link id 23946: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A pipeline to detect copy number variations (CNV) on several samples.<\/p>\n<!-- Time to render link large description section of link id 23946: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23946: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23946: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/coder.com\/docs\/code-server\" id=\"link-25652\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">code-server<\/a>\n<!-- Time to render name section of link id 25652: 3.0994415283203E-6 --> \n<\/td>\n<td>Run VSCode on any machine anywhere and access it in the browser.\n<!-- Time to render link large description section of link id 25652: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_code-server> How to use <\/a>\n<!-- Time to render notes section of link id 25652: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25652: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/Magdoll\/Cogent\" id=\"link-23997\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cogent<\/a>\n<!-- Time to render name section of link id 23997: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.<\/p>\n<!-- Time to render link large description section of link id 23997: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cogent> How to use <\/a>\n<!-- Time to render notes section of link id 23997: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23997: 0.00017881393432617 --> \n<tr><td><a href=\"https:\/\/github.com\/sokrypton\/ColabFold\" id=\"link-24900\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ColabFold<\/a>\n<!-- Time to render name section of link id 24900: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ColabFold is an easy-to-use Notebook based environment for fast and convenient protein structure predictions. Its structure prediction is powered by AlphaFold2 and RoseTTAFold combined with a fast multiple sequence alignment generation stage using MMseqs2.<\/p>\n<!-- Time to render link large description section of link id 24900: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ColabFold> How to use <\/a>\n<!-- Time to render notes section of link id 24900: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24900: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/github.com\/ziyewang\/COMEBin\" id=\"link-25576\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">COMEBin<\/a>\n<!-- Time to render name section of link id 25576: 1.9073486328125E-6 --> \n<\/td>\n<td><p>COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning.<\/p>\n<!-- Time to render link large description section of link id 25576: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_COMEBin> How to use <\/a>\n<!-- Time to render notes section of link id 25576: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25576: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/stevemussmann\/Comp-D\" id=\"link-24183\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Comp-D<\/a>\n<!-- Time to render name section of link id 24183: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A program for comprehensive computation of D-statistics and population summaries (serial version).<\/p>\n<!-- Time to render link large description section of link id 24183: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24183: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24183: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/lilit-nersisyan\/computel\" id=\"link-26019\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Computel<\/a>\n<!-- Time to render name section of link id 26019: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Computel is designed for measuring mean telomere length and abundance of canonical and variant telomeric repeats from Illumina Whole Genome NGS Sequencing data.<\/p>\n<!-- Time to render link large description section of link id 26019: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Computel> How to use <\/a>\n<!-- Time to render notes section of link id 26019: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26019: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/BinPro\/CONCOCT\" id=\"link-23870\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CONCOCT<\/a>\n<!-- Time to render name section of link id 23870: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.<\/p>\n<!-- Time to render link large description section of link id 23870: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CONCOCT> How to use <\/a>\n<!-- Time to render notes section of link id 23870: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23870: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/github.com\/mfbalin\/Concrete-Autoencoders\" id=\"link-24184\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Concrete Autoencoders<\/a>\n<!-- Time to render name section of link id 24184: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The concrete autoencoder is an end-to-end differentiable method for global feature selection, which efficiently identifies a subset of the most informative features and simultaneously learns a neural network to reconstruct the input data from the selected features.<\/p>\n<!-- Time to render link large description section of link id 24184: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24184: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24184: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/jlapaijmans\/Consensify\" id=\"link-24185\" class=\"track_this_link \" rel=\"noopener noreferrer\">Consensify<\/a>\n<!-- Time to render name section of link id 24185: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to standard pseudohaploidisation.<\/p>\n<!-- Time to render link large description section of link id 24185: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24185: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24185: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/CONSENT\" id=\"link-24079\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CONSENT<\/a>\n<!-- Time to render name section of link id 24079: 3.0994415283203E-6 --> \n<\/td>\n<td><p>CONSENT (sCalable self-cOrrectioN of long reads with multiple SEquence alignmeNT) is a self-correction method for long reads.<\/p>\n<!-- Time to render link large description section of link id 24079: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24079: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24079: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/martin-steinegger\/conterminator\" id=\"link-24800\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Conterminator<\/a>\n<!-- Time to render name section of link id 24800: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Conterminator is an efficient method for detecting incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison.<\/p>\n<!-- Time to render link large description section of link id 24800: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24800: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24800: 0.00023007392883301 --> \n<tr><td><a href=\"https:\/\/www.bio.ifi.lmu.de\/software\/contextmap\/\" id=\"link-24046\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ContextMap2<\/a>\n<!-- Time to render name section of link id 24046: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Fast and accurate context-based RNA-seq mapping. ContextMap determines the most likely origin of a read by evaluating the context of the read in the form of alignments of other reads to the same genomic region. In the original implementation, the focus was on improving initial mappings provided by other mapping tools.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24046: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24046: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24046: 0.0001990795135498 --> \n<tr><td><a href=\"http:\/\/contra.stanford.edu\/contrast\/\" id=\"link-23987\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CONTRAST<\/a>\n<!-- Time to render name section of link id 23987: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CONTRAST predicts protein-coding genes from a multiple genomic alignment using a combination of discriminative machine learning techniques.<\/p>\n<!-- Time to render link large description section of link id 23987: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23987: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23987: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/h836472\/ContScout\" id=\"link-25416\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ContScout<\/a>\n<!-- Time to render name section of link id 25416: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ContScout is a pipeline developed for the identification and removal of contaminating sequences in draft genomes.<\/p>\n<!-- Time to render link large description section of link id 25416: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ContScout> How to use <\/a>\n<!-- Time to render notes section of link id 25416: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25416: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/open2c\/cooler\" id=\"link-25261\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cooler<\/a>\n<!-- Time to render name section of link id 25261: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.<\/p>\n<!-- Time to render link large description section of link id 25261: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cooler> How to use <\/a>\n<!-- Time to render notes section of link id 25261: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25261: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/Phlya\/coolpuppy\" id=\"link-24186\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">coolpuppy<\/a>\n<!-- Time to render name section of link id 24186: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A versatile tool to perform pile-up analysis on Hi-C data in .cool format.<\/p>\n<!-- Time to render link large description section of link id 24186: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24186: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24186: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/gjeunen\/reference_database_creator\" id=\"link-25168\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRABS<\/a>\n<!-- Time to render name section of link id 25168: 2.1457672119141E-6 --> \n<\/td>\n<td><p>CRABS (Creating Reference databases for Amplicon-Based Sequencing) is a versatile software program that generates curated reference databases for metagenomic analysis.<\/p>\n<!-- Time to render link large description section of link id 25168: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CRABS> How to use <\/a>\n<!-- Time to render notes section of link id 25168: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25168: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/vibansal\/crisp\/\" id=\"link-24008\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRISP<\/a>\n<!-- Time to render name section of link id 24008: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CRISP is a software program to detect SNPs and short indels from pooled sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24008: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24008: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24008: 0.00019216537475586 --> \n<tr><td><a href=\"https:\/\/github.com\/maximilianh\/crisporWebsite\" id=\"link-24060\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRISPOR<\/a>\n<!-- Time to render name section of link id 24060: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CRISPOR predicts off-targets in the genome, ranks guides, highlights problematic guides, designs primers and helps with cloning.<\/p>\n<!-- Time to render link large description section of link id 24060: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CRISPOR> How to use <\/a>\n<!-- Time to render notes section of link id 24060: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24060: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/pinellolab\/CRISPResso2\" id=\"link-25710\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRISPResso2<\/a>\n<!-- Time to render name section of link id 25710: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CRISPResso is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Briefly, CRISPResso: aAligns sequencing reads to a reference sequence, quantifies insertions, mutations and deletions to determine whether a read is modified or unmodified by genome editing, summarizes editing results in intuitive plots and datasets.<\/p>\n<!-- Time to render link large description section of link id 25710: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CRISPResso2> How to use <\/a>\n<!-- Time to render notes section of link id 25710: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25710: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/gitlab.mbb.univ-montp2.fr\/mbb\/CroCo\" id=\"link-23900\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CroCo<\/a>\n<!-- Time to render name section of link id 23900: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification.<\/p>\n<!-- Time to render link large description section of link id 23900: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23900: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23900: 0.00017786026000977 --> \n<tr><td><a href=\"http:\/\/deweylab.biostat.wisc.edu\/csem\/\" id=\"link-24188\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">csem<\/a>\n<!-- Time to render name section of link id 24188: 2.1457672119141E-6 --> \n<\/td>\n<td><p>CSEM is a ChIP-Seq multi-read allocator. CSEM stands for ChIP-Seq multi-read allocation using Expectation-Maximization.<\/p>\n<!-- Time to render link large description section of link id 24188: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_csem> How to use <\/a>\n<!-- Time to render notes section of link id 24188: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24188: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/shenwei356\/csvtk\" id=\"link-24696\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">csvtk<\/a>\n<!-- Time to render name section of link id 24696: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A cross-platform, efficient and practical CSV\/TSV toolkit in Golang.<\/p>\n<!-- Time to render link large description section of link id 24696: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24696: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24696: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/github.com\/shenwei356\/csvtk\" id=\"link-25735\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">csvtk<\/a>\n<!-- Time to render name section of link id 25735: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A cross-platform, efficient and practical CSV\/TSV toolkit in Golang.<\/p>\n<!-- Time to render link large description section of link id 25735: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_csvtk> How to use <\/a>\n<!-- Time to render notes section of link id 25735: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25735: 0.00018596649169922 --> \n<tr><td><a href=\"http:\/\/cufflinks.cbcb.umd.edu\" id=\"link-23577\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cufflinks<\/a>\n<!-- Time to render name section of link id 23577: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.<\/p>\n<!-- Time to render link large description section of link id 23577: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cufflink> How to use <\/a>\n<!-- Time to render notes section of link id 23577: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23577: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/github.com\/esrud\/currentNe\" id=\"link-25189\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">currentNE<\/a>\n<!-- Time to render name section of link id 25189: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Estimation of current effective population using artificial neural networks.<\/p>\n<!-- Time to render link large description section of link id 25189: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_currentNe> How to use <\/a>\n<!-- Time to render notes section of link id 25189: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25189: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/cutadapt.readthedocs.io\/en\/stable\/\" id=\"link-23611\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cutadapt<\/a>\n<!-- Time to render name section of link id 23611: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.<\/p>\n<!-- Time to render link large description section of link id 23611: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cutadapt> How to use <\/a>\n<!-- Time to render notes section of link id 23611: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23611: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/tjiangHIT\/cuteSV\" id=\"link-25187\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cuteSV<\/a>\n<!-- Time to render name section of link id 25187: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Long read based human genomic structural variation detection with cuteSV.<\/p>\n<!-- Time to render link large description section of link id 25187: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cuteSV> How to use <\/a>\n<!-- Time to render notes section of link id 25187: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25187: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/brentp\/cyvcf2\" id=\"link-26029\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cyvcf2<\/a>\n<!-- Time to render name section of link id 26029: 1.9073486328125E-6 --> \n<\/td>\n<td><p>cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.<\/p>\n<!-- Time to render link large description section of link id 26029: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cyvcf2> How to use <\/a>\n<!-- Time to render notes section of link id 26029: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26029: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/kunWangkun\/d2SBin\" id=\"link-23916\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">d2SBin<\/a>\n<!-- Time to render name section of link id 23916: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Improving the binning of metagenomic contigs on d2S oligonucleotide frequency dissimilarity<\/p>\n<!-- Time to render link large description section of link id 23916: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23916: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23916: 0.00019717216491699 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/gutenkunstlab\/dadi\" id=\"link-23612\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dadi<\/a>\n<!-- Time to render name section of link id 23612: 2.1457672119141E-6 --> \n<\/td>\n<td><p>dadi implements a method for demographic inference from genetic data, based on a diffusion approximation to the allele frequency spectrum.<\/p>\n<!-- Time to render link large description section of link id 23612: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dadi> How to use <\/a>\n<!-- Time to render notes section of link id 23612: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23612: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/thegenemyers\/DALIGNER\" id=\"link-23613\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DALIGNER<\/a>\n<!-- Time to render name section of link id 23613: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The commands below permit one to find all significant local alignments between reads encoded in Dazzler database. The assumption is that the reads are from a PACBIO RS IIlong read sequencer.<\/p>\n<!-- Time to render link large description section of link id 23613: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23613: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23613: 0.00016283988952637 --> \n<tr><td><a href=\"https:\/\/github.com\/Integrative-Transcriptomics\/DamageProfiler\" id=\"link-25127\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DamageProfiler<\/a>\n<!-- Time to render name section of link id 25127: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage.<\/p>\r\n<p dir=\"auto\">DamageProfiler calculates damage profiles of mapped reads and provides a graphical as well as text based representation.<\/p>\r\n<p dir=\"auto\">It creates<\/p>\r\n<ul dir=\"auto\">\r\n\t<li>damage plots<\/li>\r\n\t<li>fragment length distribution<\/li>\r\n\t<li>read identity distribution<\/li>\r\n\t<li>base frequency table of reference<\/li>\r\n\t<li>table of different base misincorporations and their occurrences<\/li>\r\n<\/ul>\n<!-- Time to render link large description section of link id 25127: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PGDSpider> How to use <\/a>\n<!-- Time to render notes section of link id 25127: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25127: 0.00026392936706543 --> \n<tr><td><a href=\"https:\/\/github.com\/MartinPippel\/DAmar\" id=\"link-24191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAmar<\/a>\n<!-- Time to render name section of link id 24191: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Long read QC, assembly and scaffolding pipeline for PacBio or Oxford Nanopore long-read sequencing data. T he pipeline produces a number of QC metrics at various stages as well as incorporating further technologies including Bionano, 10x and HiC data to scaffold the created contigs. DAmar, is a hybrid of the earlier Marvel, Dazzler, and Daccord systems of the Eugene Myers lab.<\/p>\n<!-- Time to render link large description section of link id 24191: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24191: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24191: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/danposdoc\/\" id=\"link-23851\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DANPOS2<\/a>\n<!-- Time to render name section of link id 23851: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2<\/p>\n<!-- Time to render link large description section of link id 23851: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23851: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23851: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/ykai16\/DARIC\" id=\"link-25116\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DARIC<\/a>\n<!-- Time to render name section of link id 25116: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A complete framework for identifying quantitatively differential compartments from Hi-C and Micro-C data.<\/p>\r\n<p><code>DARIC<\/code>, or Differential Analysis for genomic Regions' Interaction with Compartments, is a computational framework to identify the quantitatively differential compartments from Hi-C-like data. For more details about the design and implementation of the framework, please check our paper published at\u00a0<a href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-023-09675-w\" rel=\"nofollow\">BMC Genomics<\/a>.<\/p>\n<!-- Time to render link large description section of link id 25116: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DARIC> How to use <\/a>\n<!-- Time to render notes section of link id 25116: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25116: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/cmks\/DAS_Tool\" id=\"link-24192\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAS_Tool<\/a>\n<!-- Time to render name section of link id 24192: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.<\/p>\n<!-- Time to render link large description section of link id 24192: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24192: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24192: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/TomWright\/dasel\" id=\"link-24774\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Dasel<\/a>\n<!-- Time to render name section of link id 24774: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Dasel (short for data-selector) allows you to query and modify data structures using selector strings.<\/p>\n<!-- Time to render link large description section of link id 24774: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24774: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24774: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/www.gnu.org\/software\/datamash\/\" id=\"link-23926\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">datamash<\/a>\n<!-- Time to render name section of link id 23926: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.<\/p>\n<!-- Time to render link large description section of link id 23926: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> default system\n<!-- Time to render notes section of link id 23926: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23926: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/github.com\/MoorjaniLab\/DATES_v4010\" id=\"link-24193\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DATES<\/a>\n<!-- Time to render name section of link id 24193: 2.1457672119141E-6 --> \n<\/td>\n<td><p>DATES (Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Narasimhan, Patterson et al. 2018<\/p>\n<!-- Time to render link large description section of link id 24193: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DATES> How to use <\/a>\n<!-- Time to render notes section of link id 24193: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24193: 0.0001838207244873 --> \n<tr><td><a href=\"https:\/\/github.com\/thegenemyers\/DAZZ_DB\" id=\"link-23614\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAZZ_DB<\/a>\n<!-- Time to render name section of link id 23614: 1.9073486328125E-6 --> \n<\/td>\n<td><p>To facilitate the multiple phases of the dazzler assembler, we organize all the read data into what is effectively a \"database\" of the reads and their meta-information.<\/p>\n<!-- Time to render link large description section of link id 23614: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23614: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23614: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/msettles\/dbcAmplicons\" id=\"link-24194\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dbcAmplicons<\/a>\n<!-- Time to render name section of link id 24194: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Analysis of Double Barcoded Illumina Amplicon Data.<\/p>\n<!-- Time to render link large description section of link id 24194: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24194: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24194: 0.00018882751464844 --> \n<tr><td><a href=\"https:\/\/github.com\/linnabrown\/run_dbcan\/\" id=\"link-25604\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dbCAN3<\/a>\n<!-- Time to render name section of link id 25604: 3.0994415283203E-6 --> \n<\/td>\n<td><p>run_dbcan (dbCAN3) is the standalone version of the dbCAN3 annotation tool for automated CAZyme annotation.<\/p>\n<!-- Time to render link large description section of link id 25604: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dbCAN3> How to use <\/a>\n<!-- Time to render notes section of link id 25604: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25604: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/yechengxi\/DBG2OLC\" id=\"link-24047\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DBG2OLC<\/a>\n<!-- Time to render name section of link id 24047: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24047: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24047: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24047: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/HIT-ImmunologyLab\/DBSCAN-SWA\/\" id=\"link-24308\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DBSCAN-SWA<\/a>\n<!-- Time to render name section of link id 24308: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An integrated tool for rapid prophage detection and annotation.<\/p>\n<!-- Time to render link large description section of link id 24308: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24308: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24308: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/LuoGroup2023\/DeChat\" id=\"link-25400\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeChat<\/a>\n<!-- Time to render name section of link id 25400: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.<\/p>\n<!-- Time to render link large description section of link id 25400: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DeChat> How to use <\/a>\n<!-- Time to render notes section of link id 25400: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25400: 0.00016283988952637 --> \n<tr><td><a href=\"https:\/\/github.com\/CamilaDuitama\/decOM\" id=\"link-25231\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">decOM<\/a>\n<!-- Time to render name section of link id 25231: 2.1457672119141E-6 --> \n<\/td>\n<td><p>decOM is a high-accuracy microbial source tracking method that is suitable for contamination quantification in paleogenomics, namely the analysis of collections of possibly contaminated ancient oral metagenomic data sets.<\/p>\n<!-- Time to render link large description section of link id 25231: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_decOM> How to use <\/a>\n<!-- Time to render notes section of link id 25231: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25231: 0.00016403198242188 --> \n<tr><td><a href=\"http:\/\/deconseq.sourceforge.net\/\" id=\"link-23878\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeconSeq<\/a>\n<!-- Time to render name section of link id 23878: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Detect and remove contaminations from your sequence data.<\/p>\n<!-- Time to render link large description section of link id 23878: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23878: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23878: 0.00024890899658203 --> \n<tr><td><a href=\"https:\/\/github.com\/champost\/DECX\" id=\"link-24082\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DECX<\/a>\n<!-- Time to render name section of link id 24082: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is the DECX (DEC eXtended) model for historical biogeographic inference<\/p>\n<!-- Time to render link large description section of link id 24082: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24082: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24082: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/apeltzer\/DeDup\" id=\"link-24196\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeDup<\/a>\n<!-- Time to render name section of link id 24196: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A merged read deduplication tool capable to perform merged read deduplication on single end data.<\/p>\n<!-- Time to render link large description section of link id 24196: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24196: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24196: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Deepbinner\" id=\"link-24010\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Deepbinner<\/a>\n<!-- Time to render name section of link id 24010: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porechop), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads.<\/p>\n<!-- Time to render link large description section of link id 24010: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24010: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24010: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfomaticsCSU\/deepsignal\" id=\"link-24197\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepSignal<\/a>\n<!-- Time to render name section of link id 24197: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Detecting methylation using signal-level features from Nanopore sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24197: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24197: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24197: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/dtu.biolib.com\/DeepTMHMM\" id=\"link-26224\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepTMHMM<\/a>\n<!-- Time to render name section of link id 26224: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A Deep Learning Model for Transmembrane Topology Prediction and Classification<\/p>\n<!-- Time to render link large description section of link id 26224: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DeepTMHMM> How to use <\/a>\n<!-- Time to render notes section of link id 26224: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26224: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/fidelram\/deepTools\" id=\"link-23866\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">deepTools<\/a>\n<!-- Time to render name section of link id 23866: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tools to process and analyze deep sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23866: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_deepTools> How to use <\/a>\n<!-- Time to render notes section of link id 23866: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23866: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/google\/deepvariant\" id=\"link-25349\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepVariant<\/a>\n<!-- Time to render name section of link id 25349: 2.8610229492188E-6 --> \n<\/td>\n<td><p>DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25349: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DeepVariant> How to use <\/a>\n<!-- Time to render notes section of link id 25349: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25349: 0.00018620491027832 --> \n<tr><td><a href=\"https:\/\/github.com\/dellytools\/delly\" id=\"link-23615\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Delly<\/a>\n<!-- Time to render name section of link id 23615: 2.1457672119141E-6 --> \n<\/td>\n<td><p>DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.<\/p>\n<!-- Time to render link large description section of link id 23615: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Delly> How to use <\/a>\n<!-- Time to render notes section of link id 23615: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23615: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/github.com\/statgen\/demuxlet\" id=\"link-24840\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">demuxlet<\/a>\n<!-- Time to render name section of link id 24840: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Genetic multiplexing of barcoded single cell RNA-seq<\/p>\n<!-- Time to render link large description section of link id 24840: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_demuxlet> How to use <\/a>\n<!-- Time to render notes section of link id 24840: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24840: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/a-ludi\/dentist\" id=\"link-24198\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DENTIST<\/a>\n<!-- Time to render name section of link id 24198: 1.9073486328125E-6 --> \n<\/td>\n<td><p>DENTIST is a sensitive, highly-accurate and automated pipeline method to close gaps in (short read) assemblies with long reads.<\/p>\n<!-- Time to render link large description section of link id 24198: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24198: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24198: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/chrisquince\/DESMAN\" id=\"link-23869\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DESMAN<\/a>\n<!-- Time to render name section of link id 23869: 3.0994415283203E-6 --> \n<\/td>\n<td><p>De novo Extraction of Strains from MetAgeNomes.<\/p>\n<!-- Time to render link large description section of link id 23869: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23869: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23869: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/cstritt\/detettore\" id=\"link-24199\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">detettore<\/a>\n<!-- Time to render name section of link id 24199: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program to detect transposable element polymorphisms<\/p>\n<!-- Time to render link large description section of link id 24199: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24199: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24199: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/devCellPy-Team\/devCellPy\" id=\"link-24805\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">devCellPy<\/a>\n<!-- Time to render name section of link id 24805: 8.1062316894531E-6 --> \n<\/td>\n<td><p>devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing (scRNA-seq).<\/p>\n<!-- Time to render link large description section of link id 24805: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_devCellPy> How to use <\/a>\n<!-- Time to render notes section of link id 24805: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24805: 0.00055098533630371 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/dfe-alpha-k-e-w\/\" id=\"link-24827\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DFE-alpha<\/a>\n<!-- Time to render name section of link id 24827: 6.9141387939453E-6 --> \n<\/td>\n<td><p>DFE-alpha was initially written to estimate the distribution of fitness effects (DFE) of new deleterious mutations using within-species nucleotide polymorphism data.<\/p>\n<!-- Time to render link large description section of link id 24827: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DFE-alpha> How to use <\/a>\n<!-- Time to render notes section of link id 24827: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24827: 0.00054597854614258 --> \n<tr><td><a href=\"https:\/\/github.com\/bbuchfink\/diamond\" id=\"link-23798\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIAMOND<\/a>\n<!-- Time to render name section of link id 23798: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Accelerated BLAST compatible local sequence aligner.<\/p>\n<!-- Time to render link large description section of link id 23798: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DIAMOND> How to use <\/a>\n<!-- Time to render notes section of link id 23798: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23798: 0.00054097175598145 --> \n<tr><td><a href=\"https:\/\/github.com\/rhysf\/DIAMOND2GO\" id=\"link-25540\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIAMOND2GO<\/a>\n<!-- Time to render name section of link id 25540: 8.1062316894531E-6 --> \n<\/td>\n<td>Diamond2GO is a set of tools that can rapidly assign gene ontology and perform enrichment for functional genomics.\n<!-- Time to render link large description section of link id 25540: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Diamond2GO> How to use <\/a>\n<!-- Time to render notes section of link id 25540: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25540: 0.00052785873413086 --> \n<tr><td><a href=\"https:\/\/git.embl.de\/grp-zaugg\/diffTF\" id=\"link-25244\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">diffTF<\/a>\n<!-- Time to render name section of link id 25244: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressor.<\/p>\n<!-- Time to render link large description section of link id 25244: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_diffTF> How to use <\/a>\n<!-- Time to render notes section of link id 25244: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25244: 0.00035309791564941 --> \n<tr><td><a href=\"https:\/\/github.com\/spyros-lytras\/dinuq\" id=\"link-24200\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DinuQ<\/a>\n<!-- Time to render name section of link id 24200: 5.0067901611328E-6 --> \n<\/td>\n<td><p>The DinuQ (Dinucleotide Quantification) Python3 package provides a range of metrics for quantifying nucleotide, dinucleotide and synonymous codon representation in genetic sequences.<\/p>\n<!-- Time to render link large description section of link id 24200: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24200: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24200: 0.00034594535827637 --> \n<tr><td><a href=\"http:\/\/www.broadinstitute.org\/software\/discovar\/blog\/\" id=\"link-24201\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Discovar<\/a>\n<!-- Time to render name section of link id 24201: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Assemble genomes and find variants with DISCOVAR &amp; DISCOVAR\u00a0de\u00a0novo<\/p>\n<!-- Time to render link large description section of link id 24201: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24201: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24201: 0.00032806396484375 --> \n<tr><td><a href=\"http:\/\/www1.montpellier.inra.fr\/CBGP\/diyabc\/\" id=\"link-23859\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIYABC<\/a>\n<!-- Time to render name section of link id 23859: 5.0067901611328E-6 --> \n<\/td>\n<td><p>A user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers.<\/p>\n<!-- Time to render link large description section of link id 23859: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23859: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23859: 0.00035786628723145 --> \n<tr><td><a href=\"https:\/\/www.cs.hmc.edu\/~yjw\/software\/dlcpar\/\" id=\"link-23820\" class=\"track_this_link \" rel=\"noopener noreferrer\">DLCpar<\/a>\n<!-- Time to render name section of link id 23820: 5.0067901611328E-6 --> \n<\/td>\n<td><p>DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).<\/p>\n<!-- Time to render link large description section of link id 23820: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DLCpar> How to use <\/a>\n<!-- Time to render notes section of link id 23820: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23820: 0.00033688545227051 --> \n<tr><td><a href=\"http:\/\/www.sigenae.org\/drap\/index.html\" id=\"link-23788\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">drap<\/a>\n<!-- Time to render name section of link id 23788: 5.0067901611328E-6 --> \n<\/td>\n<td><p>De novo RNA-seq Assembly Pipeline<\/p>\n<!-- Time to render link large description section of link id 23788: 0 --> \n<\/td>\n<td>strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DRAP> How to use <\/a>\n<!-- Time to render notes section of link id 23788: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23788: 0.00034689903259277 --> \n<tr><td><a href=\"https:\/\/github.com\/MrOlm\/drep\" id=\"link-24203\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dRep<\/a>\n<!-- Time to render name section of link id 24203: 5.0067901611328E-6 --> \n<\/td>\n<td><p>dRep is a python program for rapidly comparing large numbers of genomes. dRep can also \"de-replicate\" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.<\/p>\n<!-- Time to render link large description section of link id 24203: 7.319450378418E-5 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dRep> How to use <\/a>\n<!-- Time to render notes section of link id 24203: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24203: 0.00040912628173828 --> \n<tr><td><a href=\"https:\/\/gatb.inria.fr\/software\/dsk\/\" id=\"link-23954\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DSK<\/a>\n<!-- Time to render name section of link id 23954: 5.0067901611328E-6 --> \n<\/td>\n<td><p>DSK is a k-mer counting software, similar to Jellyfish. DSK supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. DSK can count k-mers of large Illumina datasets on laptops and desktop computers.<\/p>\n<!-- Time to render link large description section of link id 23954: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23954: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23954: 0.0003359317779541 --> \n<tr><td><a href=\"https:\/\/github.com\/millanek\/Dsuite\" id=\"link-24204\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Dsuite<\/a>\n<!-- Time to render name section of link id 24204: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations\/species<\/p>\n<!-- Time to render link large description section of link id 24204: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Dsuite> How to use <\/a>\n<!-- Time to render notes section of link id 24204: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24204: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/kcleal\/dysgu\" id=\"link-24205\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dysgu<\/a>\n<!-- Time to render name section of link id 24205: 3.0994415283203E-6 --> \n<\/td>\n<td><p>dysgu-SV is a collection of tools for calling structural variants using short or long reads.<\/p>\n<!-- Time to render link large description section of link id 24205: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dysgu> How to use <\/a>\n<!-- Time to render notes section of link id 24205: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24205: 0.0001678466796875 --> \n<tr><td><a href=\"https:\/\/github.com\/carnegie\/E2P2\" id=\"link-25295\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">E2P2<\/a>\n<!-- Time to render name section of link id 25295: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ensemble Enzyme Prediction Pipeline.<\/p>\n<!-- Time to render link large description section of link id 25295: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_E2P2> How to use <\/a>\n<!-- Time to render notes section of link id 25295: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25295: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/data.broadinstitute.org\/alkesgroup\/Eagle\/\" id=\"link-24206\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Eagle<\/a>\n<!-- Time to render name section of link id 24206: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.<\/p>\n<!-- Time to render link large description section of link id 24206: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24206: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24206: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/TobyBaril\/EarlGrey\" id=\"link-25335\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EarlGrey<\/a>\n<!-- Time to render name section of link id 25335: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A fully automated TE curation and annotation pipeline.<\/p>\n<!-- Time to render link large description section of link id 25335: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EarlGrey> How to use <\/a>\n<!-- Time to render notes section of link id 25335: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25335: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/ecopcr\/wikis\/home\" id=\"link-23616\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ecoPCR<\/a>\n<!-- Time to render name section of link id 23616: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ecoPCR is an electronic PCR software developed by LECAand Helix-Project . It helps you to estimate Barcode primers quality. In conjunction with OBItools, you can postprocess ecoPCR output to compute barcode coverage and barcode speci?city.<\/p>\n<!-- Time to render link large description section of link id 23616: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ecoPCR> How to use <\/a>\n<!-- Time to render notes section of link id 23616: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23616: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/ecoprimers\/wikis\/home\" id=\"link-23617\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ecoPrimers<\/a>\n<!-- Time to render name section of link id 23617: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ecoPrimer is a barcoding software which is written in C language. It finds universal primers from a set of input DNA sequences by finding conserved regions without \"a priori\" on candidate sequences. It also evaluates the quality of the primers and barcode regions by measuring the \"barcode specificity\" and \"barcode coverage\" indices<\/p>\n<!-- Time to render link large description section of link id 23617: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ecoPrimers> How to use <\/a>\n<!-- Time to render notes section of link id 23617: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23617: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/news\/02-06-2014-entrez-direct-released\/\" id=\"link-23825\" class=\"track_this_link \" rel=\"noopener noreferrer\">EDirect<\/a>\n<!-- Time to render name section of link id 23825: 1.8835067749023E-5 --> \n<\/td>\n<td><p>Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window<\/p>\n<!-- Time to render link large description section of link id 23825: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_Edirect> How to use <\/a>\n<!-- Time to render notes section of link id 23825: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23825: 0.00023007392883301 --> \n<tr><td><a href=\"https:\/\/github.com\/oushujun\/EDTA\" id=\"link-24208\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EDTA<\/a>\n<!-- Time to render name section of link id 24208: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.<\/p>\n<!-- Time to render link large description section of link id 24208: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EDTA> How to use <\/a>\n<!-- Time to render notes section of link id 24208: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24208: 0.00023698806762695 --> \n<tr><td><a href=\"https:\/\/github.com\/dipetkov\/eems\" id=\"link-23791\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EEMS<\/a>\n<!-- Time to render name section of link id 23791: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples.<\/p>\n<!-- Time to render link large description section of link id 23791: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EEMS> How to use <\/a>\n<!-- Time to render notes section of link id 23791: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23791: 0.00017213821411133 --> \n<tr><td><a href=\"https:\/\/github.com\/JanaSperschneider\/EffectorP-1.0\" id=\"link-25468\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EffectorP<\/a>\n<!-- Time to render name section of link id 25468: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EffectorP is a machine learning method for fungal effector prediction in secretomes and has been trained to distinguish secreted proteins from secreted effectors in plant-pathogenic fungi.<\/p>\n<!-- Time to render link large description section of link id 25468: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EffectorP> How to use <\/a>\n<!-- Time to render notes section of link id 25468: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25468: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/web2.ega-archive.org\/download\/using-ega-download-client\" id=\"link-24076\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EGA_download_client<\/a>\n<!-- Time to render name section of link id 24076: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The EgaDemoClient is a JAVA based data streamer that enables EGA account holders to securely download files and datasets, either through an interactive shell (IS) or using direct command line mode (DCLM).<\/p>\n<!-- Time to render link large description section of link id 24076: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24076: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24076: 0.00016999244689941 --> \n<tr><td><a href=\"http:\/\/egglib.sourceforge.net\" id=\"link-23618\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EggLib<\/a>\n<!-- Time to render name section of link id 23618: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EggLib is a C++\/Python library and program package for evolutionary genetics and genomics.<\/p>\n<!-- Time to render link large description section of link id 23618: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23618: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23618: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/eggnogdb\/eggnog-mapper\" id=\"link-24209\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eggNog-mapper<\/a>\n<!-- Time to render name section of link id 24209: 2.1457672119141E-6 --> \n<\/td>\n<td><p>eggnog-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only.<\/p>\n<!-- Time to render link large description section of link id 24209: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eggNOG-mapper> How to use <\/a>\n<!-- Time to render notes section of link id 24209: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24209: 0.00016903877258301 --> \n<tr><td><a href=\"http:\/\/eigen.tuxfamily.org\" id=\"link-24022\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Eigen<\/a>\n<!-- Time to render name section of link id 24022: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.<\/p>\n<!-- Time to render link large description section of link id 24022: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24022: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24022: 0.00016903877258301 --> \n<tr><td><a href=\"http:\/\/www.hsph.harvard.edu\/alkes-price\/software\/\" id=\"link-23619\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Eigensoft<\/a>\n<!-- Time to render name section of link id 23619: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).<\/p>\n<!-- Time to render link large description section of link id 23619: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EIGENSOFT> How to use <\/a>\n<!-- Time to render notes section of link id 23619: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23619: 0.00017094612121582 --> \n<tr><td><a href=\"http:\/\/www.haplotype.org\/index.html\" id=\"link-23806\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ELAI<\/a>\n<!-- Time to render name section of link id 23806: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The software performs local ancestry inference for admixed individuals.<\/p>\n<!-- Time to render link large description section of link id 23806: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ELAI> How to use <\/a>\n<!-- Time to render notes section of link id 23806: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23806: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/ExaScience\/elprep\" id=\"link-24210\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">elPrep<\/a>\n<!-- Time to render name section of link id 24210: 1.9073486328125E-6 --> \n<\/td>\n<td><p>elPrep is a high-performance tool for analyzing .sam\/.bam files (up to and including variant calling) in sequencing pipelines.<\/p>\n<!-- Time to render link large description section of link id 24210: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_elPrep> How to use <\/a>\n<!-- Time to render notes section of link id 24210: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24210: 0.00018596649169922 --> \n<tr><td><a href=\"http:\/\/meta.usc.edu\/softs\/lsa\/\" id=\"link-24013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eLSA<\/a>\n<!-- Time to render name section of link id 24013: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Extended Local Similarity Analysis -- Finding Time-Dependent Associations in Time Series Datasets<\/p>\n<!-- Time to render link large description section of link id 24013: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24013: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24013: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/arshajii\/ema\" id=\"link-24211\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMA<\/a>\n<!-- Time to render name section of link id 24211: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EMA uses a latent variable model to align barcoded short-reads (such as those produced by 10x Genomics' sequencing platform).<\/p>\n<!-- Time to render link large description section of link id 24211: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24211: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24211: 0.0001680850982666 --> \n<tr><td><a href=\"http:\/\/emboss.sourceforge.net\/\" id=\"link-23882\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMBOSS<\/a>\n<!-- Time to render name section of link id 23882: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EMBOSS is \"The European Molecular Biology Open Software Suite\". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.<\/p>\n<!-- Time to render link large description section of link id 23882: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMBOSS> How to use <\/a>\n<!-- Time to render notes section of link id 23882: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23882: 0.00024509429931641 --> \n<tr><td><a href=\"https:\/\/genome.sph.umich.edu\/wiki\/EMMAX\" id=\"link-25060\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMMAX<\/a>\n<!-- Time to render name section of link id 25060: 1.9073486328125E-6 --> \n<\/td>\n<td><p><b>EMMAX<\/b>\u00a0is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.<\/p>\n<!-- Time to render link large description section of link id 25060: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMMAX> How to use <\/a>\n<!-- Time to render notes section of link id 25060: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25060: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/treangenlab\/emu\" id=\"link-25417\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Emu<\/a>\n<!-- Time to render name section of link id 25417: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Emu is a relative abundance estimator for 16S genomic sequences. The method is optimized for error-prone full-length reads, but can also be utilized for short-read data.<\/p>\n<!-- Time to render link large description section of link id 25417: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Emu> How to use <\/a>\n<!-- Time to render notes section of link id 25417: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25417: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/enasequence\/enaBrowserTools\" id=\"link-25802\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">enaBrowserTools<\/a>\n<!-- Time to render name section of link id 25802: 2.8610229492188E-6 --> \n<\/td>\n<td><p>enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required.<\/p>\n<!-- Time to render link large description section of link id 25802: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_enaBrowserTools> How to use <\/a>\n<!-- Time to render notes section of link id 25802: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25802: 0.00041389465332031 --> \n<tr><td><a href=\"http:\/\/www.ensembl.org\/info\/docs\/api\/index.html\" id=\"link-23764\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ensembl-API<\/a>\n<!-- Time to render name section of link id 23764: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Ensembl uses MySQL relational databases to store its information. A comprehensive set of Application Programme Interfaces (APIs) serve as a middle-layer between underlying database schemes and more specific application programmes. The APIs aim to encapsulate the database layout by providing efficient high-level access to data tables and isolate applications from data layout changes. Ensembl's API is written in Perl<\/p>\n<!-- Time to render link large description section of link id 23764: 0.0005791187286377 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23764: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23764: 0.0011498928070068 --> \n<tr><td><a href=\"https:\/\/github.com\/phylo42\/EPIK\" id=\"link-25431\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EPIK<\/a>\n<!-- Time to render name section of link id 25431: 6.9141387939453E-6 --> \n<\/td>\n<td><p>EPIK is a program for rapid alignment-free phylogenetic placement.<\/p>\n<!-- Time to render link large description section of link id 25431: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EPIK> How to use <\/a>\n<!-- Time to render notes section of link id 25431: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25431: 0.00050497055053711 --> \n<tr><td><a href=\"https:\/\/erminej.msl.ubc.ca\/\" id=\"link-24215\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ErmineJ<\/a>\n<!-- Time to render name section of link id 24215: 7.8678131103516E-6 --> \n<\/td>\n<td><p>ErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies.<\/p>\n<!-- Time to render link large description section of link id 24215: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24215: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24215: 0.00050187110900879 --> \n<tr><td><a href=\"http:\/\/rssf.i2bc.paris-saclay.fr\/Software\/erpin.php\" id=\"link-24216\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">ERPIN<\/a>\n<!-- Time to render name section of link id 24216: 7.8678131103516E-6 --> \n<\/td>\n<td><p>ERPIN (Easy RNA Profile IdentificatioN) is an RNA motif search program developped by Daniel Gautheret and Andr\u00e9 Lambert.<\/p>\n<!-- Time to render link large description section of link id 24216: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24216: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24216: 0.00052309036254883 --> \n<tr><td><a href=\"https:\/\/github.com\/mtokuyama\/ERVmap\" id=\"link-24126\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ERVmap<\/a>\n<!-- Time to render name section of link id 24126: 7.1525573730469E-6 --> \n<\/td>\n<td><p>ERVmap is one part curated database of human proviral ERV loci and one part a stringent algorithm to determine which ERVs are transcribed in their RNA seq data.<\/p>\n<!-- Time to render link large description section of link id 24126: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24126: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24126: 0.00052189826965332 --> \n<tr><td><a href=\"https:\/\/github.com\/facebookresearch\/esm\" id=\"link-26206\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ESM-2<\/a>\n<!-- Time to render name section of link id 26206: 8.1062316894531E-6 --> \n<\/td>\n<td><p>This repository contains code and pre-trained weights for Transformer protein language models from the Meta Fundamental AI Research Protein Team (FAIR), including our state-of-the-art ESM-2 and ESMFold, as well as MSA Transformer, ESM-1v for predicting variant effects and ESM-IF1 for inverse folding<\/p>\n<!-- Time to render link large description section of link id 26206: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ESM-2> How to use <\/a>\n<!-- Time to render notes section of link id 26206: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26206: 0.00052809715270996 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/est-usfs\/\" id=\"link-24826\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">est-sfs<\/a>\n<!-- Time to render name section of link id 24826: 7.1525573730469E-6 --> \n<\/td>\n<td><p>est-sfs implements a maximum likelihood method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities for DNA sequence data.<\/p>\n<!-- Time to render link large description section of link id 24826: 1.1920928955078E-6 --> \n<\/td>\n<td><strong> Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24826: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24826: 0.00050115585327148 --> \n<tr><td><a href=\"https:\/\/github.com\/etetoolkit\/ete\" id=\"link-24085\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ETE<\/a>\n<!-- Time to render name section of link id 24085: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A Python framework for the analysis and visualization of trees.<\/p>\n<!-- Time to render link large description section of link id 24085: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.11.1 and <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ETE> How to use <\/a>\n<!-- Time to render notes section of link id 24085: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24085: 0.00021910667419434 --> \n<tr><td><a href=\"http:\/\/eugene.toulouse.inra.fr\/\" id=\"link-24217\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EuGeneEP<\/a>\n<!-- Time to render name section of link id 24217: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EuGene is an open integrative gene finder for eukaryotic and prokaryotic genomes. EuGene-EP (Eukaryote Pipeline) facilitates the application of EuGene on eukaryote genomes.<\/p>\n<!-- Time to render link large description section of link id 24217: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24217: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24217: 0.00023102760314941 --> \n<tr><td><a href=\"https:\/\/github.com\/Finn-Lab\/EukCC\" id=\"link-24218\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EukCC<\/a>\n<!-- Time to render name section of link id 24218: 2.8610229492188E-6 --> \n<\/td>\n<td><p>EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.<\/p>\n<!-- Time to render link large description section of link id 24218: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24218: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24218: 0.00022006034851074 --> \n<tr><td><a href=\"https:\/\/github.com\/patrickwest\/EukRep\" id=\"link-24219\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EukRep<\/a>\n<!-- Time to render name section of link id 24219: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets.<\/p>\n<!-- Time to render link large description section of link id 24219: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EukRep> How to use <\/a>\n<!-- Time to render notes section of link id 24219: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24219: 0.00022387504577637 --> \n<tr><td><a href=\"https:\/\/cgm.sjtu.edu.cn\/eupan\/\" id=\"link-24220\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EUPAN<\/a>\n<!-- Time to render name section of link id 24220: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Toolkit that integrates various software in order to build eukaryotic pangenomes.<\/p>\n<!-- Time to render link large description section of link id 24220: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24220: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24220: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/EBIvariation\/eva-sub-cli\" id=\"link-26008\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eva-sub-cli<\/a>\n<!-- Time to render name section of link id 26008: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The eva-sub-cli tool is a command line interface tool for data validation and upload.<\/p>\n<!-- Time to render link large description section of link id 26008: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eva-sub-cli> How to use <\/a>\n<!-- Time to render notes section of link id 26008: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26008: 0.00022602081298828 --> \n<tr><td><a href=\"https:\/\/github.com\/GenisGE\/evalAdmix\" id=\"link-25466\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">evalAdmix<\/a>\n<!-- Time to render name section of link id 25466: 2.8610229492188E-6 --> \n<\/td>\n<td><p>evalAdmix allows to evaluate the results of an admixture analysis (i.e. the result of applying ADMIXTURE, STRUCTURE, NGSadmix and similar).<\/p>\n<!-- Time to render link large description section of link id 25466: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_evalAdmix> How to use <\/a>\n<!-- Time to render notes section of link id 25466: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25466: 0.00023198127746582 --> \n<tr><td><a href=\"https:\/\/github.com\/OATML\/EVE\" id=\"link-25330\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EVE<\/a>\n<!-- Time to render name section of link id 25330: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EVE is a set of protein-specific models providing for any single amino acid mutation of interest a score reflecting the propensity of the resulting protein to be pathogenic.<\/p>\n<!-- Time to render link large description section of link id 25330: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EVE> How to use <\/a>\n<!-- Time to render notes section of link id 25330: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25330: 0.00022196769714355 --> \n<tr><td><a href=\"https:\/\/evidencemodeler.github.io\/\" id=\"link-23848\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EVidenceModeler (EVM)<\/a>\n<!-- Time to render name section of link id 23848: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.<\/p>\n<!-- Time to render link large description section of link id 23848: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EVidenceModeler> How to use <\/a>\n<!-- Time to render notes section of link id 23848: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23848: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/patrickbryant1\/EvoBind\" id=\"link-25625\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EvoBind<\/a>\n<!-- Time to render name section of link id 25625: 2.8610229492188E-6 --> \n<\/td>\n<td><p>EvoBind (v2) designs novel peptide binders based only on a protein target sequence. It is not necessary to specify any target residues within the protein sequence or the length of the binder (although this is possible). Cyclic binder design is also possible.<\/p>\n<!-- Time to render link large description section of link id 25625: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EvoBind> How to use <\/a>\n<!-- Time to render notes section of link id 25625: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25625: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/stamatak\/ExaML\" id=\"link-23620\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ExaML<\/a>\n<!-- Time to render name section of link id 23620: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI.<\/p>\n<!-- Time to render link large description section of link id 23620: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ExaML> How to use <\/a>\n<!-- Time to render notes section of link id 23620: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23620: 0.00022196769714355 --> \n<tr><td><a href=\"http:\/\/www.ebi.ac.uk\/about\/vertebrate-genomics\/software\/exonerate\" id=\"link-23621\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Exonerate<\/a>\n<!-- Time to render name section of link id 23621: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A generic tool for sequence alignment.<\/p>\n<!-- Time to render link large description section of link id 23621: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Exonerate> How to use <\/a>\n<!-- Time to render notes section of link id 23621: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23621: 0.0002281665802002 --> \n<tr><td><a href=\"https:\/\/pachterlab.github.io\/eXpress\/index.html\" id=\"link-23893\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eXpress<\/a>\n<!-- Time to render name section of link id 23893: 3.0994415283203E-6 --> \n<\/td>\n<td><p>eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.<\/p>\n<!-- Time to render link large description section of link id 23893: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eXpress> How to use <\/a>\n<!-- Time to render notes section of link id 23893: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23893: 0.00021791458129883 --> \n<tr><td><a href=\"https:\/\/github.com\/hasindu2008\/f5c\" id=\"link-25793\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">f5c<\/a>\n<!-- Time to render name section of link id 25793: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ultra-fast methylation calling and event alignment tool for nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25793: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_f5c> How to use <\/a>\n<!-- Time to render notes section of link id 25793: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25793: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/FABuLOUS\" id=\"link-24222\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FABuLOUS<\/a>\n<!-- Time to render name section of link id 24222: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly. Initially called TGS-GapCloser.<\/p>\n<!-- Time to render link large description section of link id 24222: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24222: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24222: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/falcon\" id=\"link-23622\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON<\/a>\n<!-- Time to render name section of link id 23622: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Falcon: a set of tools for fast aligning long reads for consensus and assembly<\/p>\n<!-- Time to render link large description section of link id 23622: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23622: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23622: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/FALCON_unzip\" id=\"link-24282\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON_unzip<\/a>\n<!-- Time to render name section of link id 24282: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Making diploid assembly becomes common practice for genomic study<\/p>\n<!-- Time to render link large description section of link id 24282: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24282: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24282: 0.00016283988952637 --> \n<tr><td><a href=\"https:\/\/github.com\/phasegenomics\/FALCON-Phase\" id=\"link-24038\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON-Phase<\/a>\n<!-- Time to render name section of link id 24038: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds.<\/p>\n<!-- Time to render link large description section of link id 24038: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24038: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24038: 0.00018501281738281 --> \n<tr><td><a href=\"http:\/\/www.pierroton.inra.fr\/genetics\/labo\/Software\/Famoz\/\" id=\"link-24224\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FaMoz<\/a>\n<!-- Time to render name section of link id 24224: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FaMoz, a software written in the C language and in TclTk, uses likelihood calculation and simulation to perform parentage studies with codominant, dominant, cytoplasmic markers or combinations of the different types.<\/p>\n<!-- Time to render link large description section of link id 24224: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24224: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24224: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/refresh-bio\/FAMSA\" id=\"link-24043\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FAMSA<\/a>\n<!-- Time to render name section of link id 24043: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM)<\/p>\n<!-- Time to render link large description section of link id 24043: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24043: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24043: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/vaquerizaslab\/fanc\" id=\"link-24225\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FAN-C<\/a>\n<!-- Time to render name section of link id 24225: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Framework for the ANalysis of C-like data.<\/p>\n<!-- Time to render link large description section of link id 24225: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FAN-C> How to use <\/a>\n<!-- Time to render notes section of link id 24225: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24225: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/www.microsoft.com\/en-us\/download\/details.aspx?id=52559\" id=\"link-24226\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FaST-LMM<\/a>\n<!-- Time to render name section of link id 24226: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a program for performing genome-wide association studies (GWAS) on large data sets.<\/p>\n<!-- Time to render link large description section of link id 24226: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24226: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24226: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/mrmckain\/Fast-Plast\" id=\"link-24227\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Fast-Plast<\/a>\n<!-- Time to render name section of link id 24227: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and verify whole chloroplast genome sequences.<\/p>\n<!-- Time to render link large description section of link id 24227: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24227: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24227: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/fasta.bioch.virginia.edu\/fasta_www2\/fasta_list2.shtml\" id=\"link-23623\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTA<\/a>\n<!-- Time to render name section of link id 23623: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FASTA is a sequence similarity search tool which uses heuristics for fast local alignment searching.<\/p>\n<!-- Time to render link large description section of link id 23623: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTA> How to use <\/a>\n<!-- Time to render notes section of link id 23623: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23623: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/CBBresearch\/Spouge\/html_ncbi\/html\/fasta\/composition.html\" id=\"link-23991\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTA Composition<\/a>\n<!-- Time to render name section of link id 23991: 3.0994415283203E-6 --> \n<\/td>\n<td><p>finds the overall composition of sequences in a FASTA file<\/p>\n<!-- Time to render link large description section of link id 23991: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTA_Composition> How to use <\/a>\n<!-- Time to render notes section of link id 23991: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23991: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/CBBresearch\/Spouge\/html_ncbi\/html\/software\/program.html?uid=10\" id=\"link-23933\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTA_Length<\/a>\n<!-- Time to render name section of link id 23933: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FASTA Length finds the lengths of sequences in a FASTA file.<\/p>\n<!-- Time to render link large description section of link id 23933: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTA_Length> How to use <\/a>\n<!-- Time to render notes section of link id 23933: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23933: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/linsalrob\/fasta_validator\" id=\"link-25522\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fasta_validator<\/a>\n<!-- Time to render name section of link id 25522: 1.9073486328125E-6 --> \n<\/td>\n<td><p>C code to validate a fasta file.<\/p>\n<!-- Time to render link large description section of link id 25522: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fasta_validator> How to use <\/a>\n<!-- Time to render notes section of link id 25522: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25522: 0.00016093254089355 --> \n<tr><td><a href=\"https:\/\/bioinfo.ut.ee\/?page_id=167\" id=\"link-24228\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastaGrep<\/a>\n<!-- Time to render name section of link id 24228: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. It can do both match\/mismatch based and thermodynamic binding energy searches.<\/p>\n<!-- Time to render link large description section of link id 24228: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24228: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24228: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/ParBLiSS\/FastANI\" id=\"link-24124\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastANI<\/a>\n<!-- Time to render name section of link id 24124: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)<\/p>\n<!-- Time to render link large description section of link id 24124: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastANI> How to use <\/a>\n<!-- Time to render notes section of link id 24124: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24124: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/fastix\" id=\"link-25004\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastix<\/a>\n<!-- Time to render name section of link id 25004: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A simple command line tool to add prefixes to FASTA headers.<\/p>\n<!-- Time to render link large description section of link id 25004: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastix> How to use <\/a>\n<!-- Time to render notes section of link id 25004: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25004: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/fastk-medians\" id=\"link-25442\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastk-medians<\/a>\n<!-- Time to render name section of link id 25442: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of utilities to calculate the median number of times the k-mers in a sequence of interest occur across the whole set.<\/p>\n<!-- Time to render link large description section of link id 25442: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastk-medians> How to use <\/a>\n<!-- Time to render notes section of link id 25442: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25442: 0.00016021728515625 --> \n<tr><td><a href=\"http:\/\/www.atgc-montpellier.fr\/fastme\/\" id=\"link-23819\" class=\"track_this_link \" rel=\"noopener noreferrer\">FastME<\/a>\n<!-- Time to render name section of link id 23819: 2.1457672119141E-6 --> \n<\/td>\n<td><p>FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of NJ. FastME improves over NJ by performing topological moves using fast, sophisticated algorithms.<\/p>\n<!-- Time to render link large description section of link id 23819: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastME> How to use <\/a>\n<!-- Time to render notes section of link id 23819: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23819: 0.00018978118896484 --> \n<tr><td><a href=\"https:\/\/github.com\/e-jorsboe\/fastNGSadmix\" id=\"link-24229\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastNGSadmix<\/a>\n<!-- Time to render name section of link id 24229: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Program for infering admixture proportions and doing PCA with a single NGS sample. Inferences based on reference panel.<\/p>\n<!-- Time to render link large description section of link id 24229: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24229: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24229: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/OpenGene\/fastp\" id=\"link-23988\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastp<\/a>\n<!-- Time to render name section of link id 23988: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool designed to provide fast all-in-one preprocessing for FastQ files.<\/p>\n<!-- Time to render link large description section of link id 23988: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastp> How to use <\/a>\n<!-- Time to render notes section of link id 23988: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23988: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/bioinformaticshome.com\/tools\/imputation\/descriptions\/fastPHASE.html\" id=\"link-24230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastPHASE<\/a>\n<!-- Time to render name section of link id 24230: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool for genotype imputation and estimating missing haplotypes.<\/p>\n<!-- Time to render link large description section of link id 24230: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24230: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24230: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/OpenGene\/fastplong\" id=\"link-25596\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastplong<\/a>\n<!-- Time to render name section of link id 25596: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ultra-fast preprocessing and quality control for long-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25596: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastplong> How to use <\/a>\n<!-- Time to render notes section of link id 25596: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25596: 0.00016522407531738 --> \n<tr><td><a href=\"https:\/\/rostlab.org\/owiki\/index.php\/Fastprofkernel\" id=\"link-24068\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastprofkernel<\/a>\n<!-- Time to render name section of link id 24068: 2.8610229492188E-6 --> \n<\/td>\n<td><p>fastprofkernel is a Debian package that uses an accelerated version of the original profile kernel <1> to automatically train SVM based classification models. It can assign user-defined classes to so far uncharacterized proteins.<\/p>\n<!-- Time to render link large description section of link id 24068: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastprofkernel> How to use <\/a>\n<!-- Time to render notes section of link id 24068: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24068: 0.00018095970153809 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastq_screen\/\" id=\"link-23834\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastQ Screen<\/a>\n<!-- Time to render name section of link id 23834: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.<\/p>\n<!-- Time to render link large description section of link id 23834: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastQScreen> How to use <\/a>\n<!-- Time to render notes section of link id 23834: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23834: 0.0001988410949707 --> \n<tr><td><a href=\"http:\/\/cancan.cshl.edu\/labmembers\/gordon\/fastq_illumina_filter\/\" id=\"link-23894\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastq_illumina_filter<\/a>\n<!-- Time to render name section of link id 23894: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This program can filter FASTQ files produced by CASAVA 1.8, and keep\/discard reads based on this filter flag.<\/p>\n<!-- Time to render link large description section of link id 23894: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastq_illumina_filter> How to use <\/a>\n<!-- Time to render notes section of link id 23894: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23894: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/homes.cs.washington.edu\/~dcjones\/fastq-tools\/\" id=\"link-24231\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastq-tools<\/a>\n<!-- Time to render name section of link id 24231: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.<\/p>\n<!-- Time to render link large description section of link id 24231: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24231: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24231: 0.00016188621520996 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/\" id=\"link-23624\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastQC<\/a>\n<!-- Time to render name section of link id 23624: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Quality Control application for FastQ files. FastQC is an application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report.<\/p>\n<!-- Time to render link large description section of link id 23624: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastQC> How to use <\/a>\n<!-- Time to render notes section of link id 23624: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23624: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/statgen\/fastQValidator\" id=\"link-24122\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastQValidator<\/a>\n<!-- Time to render name section of link id 24122: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The fastQValidator validates the format of fastq files<\/p>\n<!-- Time to render link large description section of link id 24122: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24122: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24122: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/nicofmay\/fastsimbac\" id=\"link-24021\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastSimBac<\/a>\n<!-- Time to render name section of link id 24021: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastSimBac is a simulator of the coalescent process with bacterial recombination that simulates genealogies spatially across chromosomes as a Markov process.<\/p>\n<!-- Time to render link large description section of link id 24021: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24021: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24021: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/cmpg.unibe.ch\/software\/fastsimcoal2\/\" id=\"link-23625\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastsimcoal2<\/a>\n<!-- Time to render name section of link id 23625: 1.6927719116211E-5 --> \n<\/td>\n<td><p>Fast sequential Markov coalescent simulation of genomic data under complex evolutionary models<\/p>\n<!-- Time to render link large description section of link id 23625: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastsimcoal2> How to use <\/a>\n<!-- Time to render notes section of link id 23625: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23625: 0.00029087066650391 --> \n<tr><td><a href=\"http:\/\/rajanil.github.io\/fastStructure\/\" id=\"link-23626\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastStructure<\/a>\n<!-- Time to render name section of link id 23626: 3.0994415283203E-6 --> \n<\/td>\n<td><p>fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.<\/p>\n<!-- Time to render link large description section of link id 23626: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastStructure> How to use <\/a>\n<!-- Time to render notes section of link id 23626: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23626: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/www.microbesonline.org\/fasttree\/\" id=\"link-23774\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastTree<\/a>\n<!-- Time to render name section of link id 23774: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.<\/p>\n<!-- Time to render link large description section of link id 23774: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastTree> How to use <\/a>\n<!-- Time to render notes section of link id 23774: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23774: 0.00016379356384277 --> \n<tr><td><a href=\"http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/\" id=\"link-23627\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTX-Toolkit<\/a>\n<!-- Time to render name section of link id 23627: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA\/FASTQ files preprocessing.<\/p>\n<!-- Time to render link large description section of link id 23627: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTX-Toolkit> How to use <\/a>\n<!-- Time to render notes section of link id 23627: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23627: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/view\/fbat-web-page\" id=\"link-23967\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FBAT<\/a>\n<!-- Time to render name section of link id 23967: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FBAT is an acronym for Family-Based Association Tests in genetic analyses. Family-based association designs, as opposed to case-control study designs, are particularly attractive, since they test for linkage as well as association, avoid spurious associations caused by admixture of populations, and are convenient for investigators interested in refining linkage findings in family samples.<\/p>\n<!-- Time to render link large description section of link id 23967: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23967: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23967: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/fcs\" id=\"link-25990\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FCS<\/a>\n<!-- Time to render name section of link id 25990: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The NCBI Foreign Contamination Screen (FCS) is a tool suite (FCS-adaptator et FCS-gx) for identifying and removing contaminant sequences in genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 25990: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FCS> How to use <\/a>\n<!-- Time to render notes section of link id 25990: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25990: 0.00016093254089355 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/fcs-gx\" id=\"link-25536\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FCS-GX<\/a>\n<!-- Time to render name section of link id 25536: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FCS-GX detects contamination from foreign organisms in genome sequences. This tool is one module within the NCBI Foreign Contamination Screening (FCS) program suite.<\/p>\n<!-- Time to render link large description section of link id 25536: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FCS-GX> How to use <\/a>\n<!-- Time to render notes section of link id 25536: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25536: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/tderrien\/FEELnc\" id=\"link-23778\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FEELnc<\/a>\n<!-- Time to render name section of link id 23778: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FlExible Extraction of LncRNA.<\/p>\n<!-- Time to render link large description section of link id 23778: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FEELnc> How to use <\/a\n<!-- Time to render notes section of link id 23778: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23778: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/ffmpeg.org\" id=\"link-25643\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FFmpeg<\/a>\n<!-- Time to render name section of link id 25643: 1.9073486328125E-6 --> \n<\/td>\n<td>FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created.\n<!-- Time to render link large description section of link id 25643: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FFmpeg> How to use <\/a>\n<!-- Time to render notes section of link id 25643: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25643: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/fulcrumgenomics\/fgbio\" id=\"link-24040\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fgbio<\/a>\n<!-- Time to render name section of link id 24040: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of tools to analyze genomic data with a focus on Next Generation Sequencing.<\/p>\n<!-- Time to render link large description section of link id 24040: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24040: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24040: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/github.com\/rambaut\/figtree\" id=\"link-25257\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FigTree<\/a>\n<!-- Time to render name section of link id 25257: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.<\/p>\n<!-- Time to render link large description section of link id 25257: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FigTree> How to use <\/a>\n<!-- Time to render notes section of link id 25257: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25257: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Filtlong\" id=\"link-24232\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Filtlong<\/a>\n<!-- Time to render name section of link id 24232: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Filtlong is a tool for filtering long reads by quality.<\/p>\n<!-- Time to render link large description section of link id 24232: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Filtlong> How to use <\/a>\n<!-- Time to render notes section of link id 24232: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24232: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/DjampaKozlowski\/FindingOverCovRegions\" id=\"link-24234\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FindingOverCovRegions<\/a>\n<!-- Time to render name section of link id 24234: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FindOverCovRegions.py search for genomic regions with abnormal read coverage (e.g. depth). To do so, this program requieres begraph-like file (e.g. bedtools genomecov per-base reports) where for each position of the genome, the coverage depth is reported (even 0 values).<\/p>\n<!-- Time to render link large description section of link id 24234: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24234: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24234: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/millanek\/fineRADstructure\" id=\"link-24235\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fineRADstructure<\/a>\n<!-- Time to render name section of link id 24235: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A complete, easy to use, and fast population inference package for RAD-seq data.<\/p>\n<!-- Time to render link large description section of link id 24235: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24235: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24235: 0.00018501281738281 --> \n<tr><td><a href=\"http:\/\/www.paintmychromosomes.com\/\" id=\"link-23628\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fineSTRUCTURE<\/a>\n<!-- Time to render name section of link id 23628: 3.0994415283203E-6 --> \n<\/td>\n<td><p>fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23628: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fineSTRUCTURE> How to use <\/a>\n<!-- Time to render notes section of link id 23628: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23628: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/BrooksLabUCSC\/flair\" id=\"link-24236\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAIR<\/a>\n<!-- Time to render name section of link id 24236: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24236: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24236: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24236: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/LuyiTian\/FLAMES\" id=\"link-25920\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAMES<\/a>\n<!-- Time to render name section of link id 25920: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Full-length transcriptome splicing and mutation analysis.<\/p>\n<!-- Time to render link large description section of link id 25920: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FLAMES> How to use <\/a>\n<!-- Time to render notes section of link id 25920: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25920: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/browning-lab\/flare\" id=\"link-25560\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">flare<\/a>\n<!-- Time to render name section of link id 25560: 1.9073486328125E-6 --> \n<\/td>\n<td>The flare program uses a set of reference haplotypes to infer the ancestry of each allele in a set of admixed study samples. The flare program is fast, accurate, and memory-efficient.\n<!-- Time to render link large description section of link id 25560: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_flare> How to use <\/a>\n<!-- Time to render notes section of link id 25560: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25560: 0.00036406517028809 --> \n<tr><td><a href=\"https:\/\/github.com\/baoe\/FLAS\" id=\"link-24096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAS<\/a>\n<!-- Time to render name section of link id 24096: 7.1525573730469E-6 --> \n<\/td>\n<td><p>FLAS is software that makes self-correction for PacBio long reads with fast speed and high throughput.<\/p>\n<!-- Time to render link large description section of link id 24096: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24096: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24096: 0.00052809715270996 --> \n<tr><td><a href=\"http:\/\/www.cbcb.umd.edu\/software\/flash\" id=\"link-23629\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLASH<\/a>\n<!-- Time to render name section of link id 23629: 7.1525573730469E-6 --> \n<\/td>\n<td><p>FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 23629: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FLASH> How to use <\/a>\n<!-- Time to render notes section of link id 23629: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23629: 0.00052094459533691 --> \n<tr><td><a href=\"https:\/\/github.com\/seqan\/flexbar\" id=\"link-23630\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Flexbar<\/a>\n<!-- Time to render name section of link id 23630: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta\/q and csfasta\/q format from Illumina, Roche 454, and the SOLiD platform.<\/p>\n<!-- Time to render link large description section of link id 23630: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Flexbar> How to use <\/a>\n<!-- Time to render notes section of link id 23630: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23630: 0.00055408477783203 --> \n<tr><td><a href=\"https:\/\/github.com\/fenderglass\/Flye\" id=\"link-24015\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Flye<\/a>\n<!-- Time to render name section of link id 24015: 7.8678131103516E-6 --> \n<\/td>\n<td><p>Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.<\/p>\n<!-- Time to render link large description section of link id 24015: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Flye> How to use <\/a>\n<!-- Time to render notes section of link id 24015: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24015: 0.00058221817016602 --> \n<tr><td><a href=\"https:\/\/github.com\/holtjma\/fmlrc\" id=\"link-24237\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FMLRC<\/a>\n<!-- Time to render name section of link id 24237: 6.9141387939453E-6 --> \n<\/td>\n<td><p>FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24237: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24237: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24237: 0.00054502487182617 --> \n<tr><td><a href=\"https:\/\/github.com\/jwanglab\/fmlrc2\" id=\"link-25112\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FMLRC2<\/a>\n<!-- Time to render name section of link id 25112: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FMLRC2 performs error correction\/polishing of long erroneous sequences with accurate short reads. As such, it can be used as\u00a0<em>both<\/em>\u00a0an error-correction tool <<a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2051-3\" rel=\"nofollow\">1<\/a>> for raw long reads (ex. Oxford Nanopore)\u00a0<em>and<\/em>\u00a0a polishing tool <<a href=\"http:\/\/biorxiv.org\/content\/early\/2022\/07\/23\/2022.07.22.501182\" rel=\"nofollow\">2<\/a>> for\u00a0<em>de novo<\/em>\u00a0assemblies.<\/p>\n<!-- Time to render link large description section of link id 25112: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FMLRC2> How to use <\/a>\n<!-- Time to render notes section of link id 25112: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25112: 0.00025296211242676 --> \n<tr><td><a href=\"https:\/\/github.com\/natir\/fpa\" id=\"link-24101\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fpa<\/a>\n<!-- Time to render name section of link id 24101: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Filter Pairwise Alignment<\/p>\n<!-- Time to render link large description section of link id 24101: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24101: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24101: 0.00022387504577637 --> \n<tr><td><a href=\"https:\/\/github.com\/alastair-droop\/fqtools\" id=\"link-23952\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fqtools<\/a>\n<!-- Time to render name section of link id 23952: 2.8610229492188E-6 --> \n<\/td>\n<td><p>fqtools is a software suite for fast processing of FASTQ files; Various file manipulations are supported.<\/p>\n<!-- Time to render link large description section of link id 23952: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23952: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23952: 0.00022482872009277 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/fraggenescan\/\" id=\"link-23937\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FragGeneScan<\/a>\n<!-- Time to render name section of link id 23937: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.<\/p>\n<!-- Time to render link large description section of link id 23937: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23937: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23937: 0.00024199485778809 --> \n<tr><td><a href=\"https:\/\/github.com\/unipept\/FragGeneScanRs\" id=\"link-25302\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FragGeneScanRs<\/a>\n<!-- Time to render name section of link id 25302: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FragGeneScanRs is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.<\/p>\r\n<p>It is a re-implementation of FragGeneScan in Rust.<\/p>\n<!-- Time to render link large description section of link id 25302: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FragGeneScanRs> How to use <\/a>\n<!-- Time to render notes section of link id 25302: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25302: 0.00033402442932129 --> \n<tr><td><a href=\"https:\/\/github.com\/tkchafin\/fragmatic\" id=\"link-24239\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fragmatic<\/a>\n<!-- Time to render name section of link id 24239: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Simple program for in silico restriction digest of genomic sequences, to simulate RAD-family NGS library prep methods.<\/p>\n<!-- Time to render link large description section of link id 24239: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24239: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24239: 0.00022387504577637 --> \n<tr><td><a href=\"https:\/\/github.com\/rdpstaff\/Framebot\" id=\"link-23711\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FrameBot<\/a>\n<!-- Time to render name section of link id 23711: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RDP FrameBot is a tool for correcting frameshift errors caused by insertions and deletions in DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 23711: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23711: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23711: 0.00022792816162109 --> \n<tr><td><a href=\"https:\/\/iant.toulouse.inra.fr\/\/FrameDP\/\" id=\"link-23631\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FrameDP<\/a>\n<!-- Time to render name section of link id 23631: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Sensitive peptide detection on noisy matured sequences. Available with command line interface on the cluster.<\/p>\n<!-- Time to render link large description section of link id 23631: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23631: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23631: 0.00022196769714355 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/freebayes\" id=\"link-23980\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FreeBayes<\/a>\n<!-- Time to render name section of link id 23980: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.<\/p>\n<!-- Time to render link large description section of link id 23980: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_freebayes> How to use <\/a>\n<!-- Time to render notes section of link id 23980: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23980: 0.00022292137145996 --> \n<tr><td><a href=\"https:\/\/funannotate.readthedocs.io\/en\/latest\/index.html\" id=\"link-24241\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Funannotate<\/a>\n<!-- Time to render name section of link id 24241: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Funannotate is a genome prediction, annotation, and comparison software package.<\/p>\n<!-- Time to render link large description section of link id 24241: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Funannotate> How to use <\/a>\n<!-- Time to render notes section of link id 24241: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24241: 0.00022292137145996 --> \n<tr><td><a href=\"https:\/\/github.com\/gphocs-dev\/G-PhoCS\" id=\"link-25558\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">G-PhoCS<\/a>\n<!-- Time to render name section of link id 25558: 2.1457672119141E-6 --> \n<\/td>\n<td>G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.\n<!-- Time to render link large description section of link id 25558: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_G-PhoCS> How to use <\/a>\n<!-- Time to render notes section of link id 25558: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25558: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/lidaof\/g3d\" id=\"link-25033\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">g3d<\/a>\n<!-- Time to render name section of link id 25033: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Genomics 3D visualizer tool sets.<\/p>\r\n<p><code class=\"docutils literal notranslate\"><span class=\"pre\">g3d<\/span><\/code>\u00a0is a binary file format for storing genomic 3D structure data,\u00a0<code class=\"docutils literal notranslate\"><span class=\"pre\">g3d<\/span><\/code>\u00a0is short for genomic 3D format.<\/p>\n<!-- Time to render link large description section of link id 25033: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_g3d> How to use <\/a>\n<!-- Time to render notes section of link id 25033: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25033: 0.00022983551025391 --> \n<tr><td><a href=\"https:\/\/github.com\/NBISweden\/GAAS\" id=\"link-24242\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GAAS<\/a>\n<!-- Time to render name section of link id 24242: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Genome Assembly Annotation Service: Suite of tools related to Genome Assembly Annotation Service tasks.<\/p>\n<!-- Time to render link large description section of link id 24242: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24242: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24242: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/GALBA\" id=\"link-24602\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GALBA<\/a>\n<!-- Time to render name section of link id 24602: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available.<\/p>\n<!-- Time to render link large description section of link id 24602: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24602: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24602: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/regevs\/gamma_smc\" id=\"link-25135\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gamma-SMC<\/a>\n<!-- Time to render name section of link id 25135: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This is an alternative and an upgrade of the widely used PSMC method, which infers population size trajectories from VCF files.<\/p>\n<!-- Time to render link large description section of link id 25135: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gamma-SMC> How to use <\/a>\n<!-- Time to render notes section of link id 25135: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25135: 0.00020480155944824 --> \n<tr><td><a href=\"http:\/\/soap.genomics.org.cn\/about.html#resource2\" id=\"link-23633\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GapCloser<\/a>\n<!-- Time to render name section of link id 23633: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo, using the abundant pair relationships of short reads.<\/p>\n<!-- Time to render link large description section of link id 23633: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GapCloser> How to use <\/a>\n<!-- Time to render notes section of link id 23633: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23633: 0.0001678466796875 --> \n<tr><td><a href=\"https:\/\/github.com\/lczech\/gappa\" id=\"link-25572\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gappa<\/a>\n<!-- Time to render name section of link id 25572: 1.9073486328125E-6 --> \n<\/td>\n<td>A toolkit for analyzing and visualizing phylogenetic (placement) data.\n<!-- Time to render link large description section of link id 25572: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gappa> How to use <\/a>\n<!-- Time to render notes section of link id 25572: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25572: 0.00016880035400391 --> \n<tr><td><a href=\"https:\/\/github.com\/jotech\/gapseq\" id=\"link-26234\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gapseq<\/a>\n<!-- Time to render name section of link id 26234: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks.<\/p>\n<!-- Time to render link large description section of link id 26234: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gapseq> How to use <\/a>\n<!-- Time to render notes section of link id 26234: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26234: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/gargammel\" id=\"link-23815\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gargammel<\/a>\n<!-- Time to render name section of link id 23815: 1.9073486328125E-6 --> \n<\/td>\n<td><p>gargammel is an ancient DNA simulator<\/p>\n<!-- Time to render link large description section of link id 23815: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gargammel> How to use <\/a>\n<!-- Time to render notes section of link id 23815: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23815: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/zwickl\/garli\" id=\"link-24091\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GARLI<\/a>\n<!-- Time to render name section of link id 24091: 3.0994415283203E-6 --> \n<\/td>\n<td><p>GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees.<\/p>\n<!-- Time to render link large description section of link id 24091: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24091: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24091: 0.00019693374633789 --> \n<tr><td><a href=\"http:\/\/www.broadinstitute.org\/gsa\/wiki\/index.php\/The_Genome_Analysis_Toolkit\" id=\"link-23634\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GATK<\/a>\n<!-- Time to render name section of link id 23634: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP\/indel caller and a local realigner.<\/p>\n<!-- Time to render link large description section of link id 23634: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GATK> How to use <\/a>\n<!-- Time to render notes section of link id 23634: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23634: 0.00020003318786621 --> \n<tr><td><a href=\"http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks.html\" id=\"link-23765\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gblocks<\/a>\n<!-- Time to render name section of link id 23765: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. These positions may not be homologous or may have been saturated by multiple substitutions and it is convenient to eliminate them prior to phylogenetic analysis.<\/p>\n<!-- Time to render link large description section of link id 23765: 1.6927719116211E-5 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gblocks> How to use <\/a>\n<!-- Time to render notes section of link id 23765: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23765: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/yeeus\/GCI.git\" id=\"link-25561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GCI<\/a>\n<!-- Time to render name section of link id 25561: 2.1457672119141E-6 --> \n<\/td>\n<td>Genome Continuity Inspector (GCI) is an assembly assessment tool for high-quality genomes (e.g. T2T genomes), in base resolution.\n<!-- Time to render link large description section of link id 25561: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCI> How to use <\/a>\n<!-- Time to render notes section of link id 25561: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25561: 0.0001678466796875 --> \n<tr><td><a href=\"https:\/\/cloud.google.com\/sdk\/docs\/install?hl=fr\" id=\"link-26217\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gcloud<\/a>\n<!-- Time to render name section of link id 26217: 1.9073486328125E-6 --> \n<\/td>\n<td><p>gcloud CLI is a set of tools for creating and managing Google Cloud resources.<\/p>\n<!-- Time to render link large description section of link id 26217: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gcloud> How to use <\/a>\n<!-- Time to render notes section of link id 26217: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26217: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/bioinfo2.ugr.es\/gCluster\/\" id=\"link-25513\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gCluster<\/a>\n<!-- Time to render name section of link id 25513: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The gCluster algorithm is a general clustering method that predicts clusters of any biological word or combination of them, relying only on the DNA sequence and the statistical significance. When using CG as word, gCluster works similarly to CpGcluster, our method to predict CpG islands. More broadly, gCluster has much in common with wordCluster but uses an improved distance model.<\/p>\n<!-- Time to render link large description section of link id 25513: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gCluster> How to use <\/a>\n<!-- Time to render notes section of link id 25513: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25513: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/yanglab.westlake.edu.cn\/software\/gcta\/#Overview\" id=\"link-23830\" class=\"track_this_link \" rel=\"noopener noreferrer\">GCTA<\/a>\n<!-- Time to render name section of link id 23830: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.<\/p>\n<!-- Time to render link large description section of link id 23830: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCTA> How to use <\/a>\n<!-- Time to render notes section of link id 23830: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23830: 0.00019192695617676 --> \n<tr><td><a href=\"http:\/\/www.gdal.org\/\" id=\"link-23789\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GDAL<\/a>\n<!-- Time to render name section of link id 23789: 3.0994415283203E-6 --> \n<\/td>\n<td><p>a translator library for raster and vector geospatial data formats that is released under an X\/MIT style Open Source license by the Open Source Geospatial Foundation.<\/p>\n<!-- Time to render link large description section of link id 23789: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23789: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23789: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/groups.csail.mit.edu\/cgs\/gem\/\" id=\"link-25246\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEM<\/a>\n<!-- Time to render name section of link id 25246: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GEM is a scientific software for studying protein-DNA interaction at high resolution using ChIP-seq\/ChIP-exo data. It can also be applied to CLIP-seq and Branch-seq data.<\/p>\n<!-- Time to render link large description section of link id 25246: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEM> How to use <\/a>\n<!-- Time to render notes section of link id 25246: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25246: 0.0001678466796875 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/gemlibrary\/\" id=\"link-25030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEM-library<\/a>\n<!-- Time to render name section of link id 25030: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of very optimized tools for indexing\/querying huge genomes\/files.<\/p>\n<!-- Time to render link large description section of link id 25030: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEM-library> How to use <\/a>\n<!-- Time to render notes section of link id 25030: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25030: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/gemtools\/gemtools\" id=\"link-25103\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEM-Tools<\/a>\n<!-- Time to render name section of link id 25103: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.<\/p>\n<!-- Time to render link large description section of link id 25103: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEM-Tools> How to use <\/a>\n<!-- Time to render notes section of link id 25103: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25103: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/heathsc\/gemBS-rs\" id=\"link-24243\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gemBS<\/a>\n<!-- Time to render name section of link id 24243: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gemBS is a high performance bioinformatic pipeline designed for highthroughput analysis of DNA methylation data from whole genome bisulfites sequencing data (WGBS). It combines GEM3, a high performance read aligner and bs_call, a high performance variant and methyation caller, into a streamlined and efficient pipeline for bisulfite sequence analysis.<\/p>\n<!-- Time to render link large description section of link id 24243: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gemBS> How to use <\/a>\n<!-- Time to render notes section of link id 24243: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24243: 0.0002589225769043 --> \n<tr><td><a href=\"http:\/\/www.xzlab.org\/software.html\" id=\"link-23635\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEMMA<\/a>\n<!-- Time to render name section of link id 23635: 2.8610229492188E-6 --> \n<\/td>\n<td><p>GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS).<\/p>\n<!-- Time to render link large description section of link id 23635: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEMMA> How to use <\/a>\n<!-- Time to render notes section of link id 23635: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23635: 0.00019502639770508 --> \n<tr><td><a href=\"http:\/\/www.jstacs.de\/index.php\/GeMoMa\" id=\"link-24244\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeMoMa<\/a>\n<!-- Time to render name section of link id 24244: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Gene Model Mapper (GeMoMa) is a homology-based gene prediction program.<\/p>\n<!-- Time to render link large description section of link id 24244: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24244: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24244: 0.00018191337585449 --> \n<tr><td><a href=\"http:\/\/genome.crg.es\/software\/geneid\/\" id=\"link-23950\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">geneid<\/a>\n<!-- Time to render name section of link id 23950: 2.1457672119141E-6 --> \n<\/td>\n<td><p>geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.<\/p>\n<!-- Time to render link large description section of link id 23950: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_geneid> How to use <\/a>\n<!-- Time to render notes section of link id 23950: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23950: 0.00016212463378906 --> \n<tr><td><a href=\"http:\/\/opal.biology.gatech.edu\/GeneMark\/\" id=\"link-23863\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneMark-ES<\/a>\n<!-- Time to render name section of link id 23863: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Unsupervised training is an important feature of the GeneMark-ES algorithm that identifies protein coding genes in eukaryotic genomes. This is the only eukaryotic gene finder that can perform gene prediction without curated training sets.<\/p>\n<!-- Time to render link large description section of link id 23863: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GeneMark> How to use <\/a>\n<!-- Time to render notes section of link id 23863: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23863: 0.00019192695617676 --> \n<tr><td><a href=\"http:\/\/opal.biology.gatech.edu\/GeneMark\/\" id=\"link-23636\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneMark-ET<\/a>\n<!-- Time to render name section of link id 23636: 2.1457672119141E-6 --> \n<\/td>\n<td><p>a semi-supervised version of GeneMark-ES, called GeneMark-ET that uses RNA-Seq reads to improve training.<\/p>\n<!-- Time to render link large description section of link id 23636: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GeneMark> How to use <\/a>\n<!-- Time to render notes section of link id 23636: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23636: 0.00020003318786621 --> \n<tr><td><a href=\"https:\/\/kimura.univ-montp2.fr\/~rousset\/Genepop.htm\" id=\"link-24246\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Genepop<\/a>\n<!-- Time to render name section of link id 24246: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Population genetics software that computes estimates of F-statistics.<\/p>\n<!-- Time to render link large description section of link id 24246: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24246: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24246: 0.0001671314239502 --> \n<tr><td><a href=\"https:\/\/github.com\/BrendelGroup\/GeneSeqer\" id=\"link-24247\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneSeqer<\/a>\n<!-- Time to render name section of link id 24247: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Sensitive spliced-alignment of cDNAs or proteins.<\/p>\n<!-- Time to render link large description section of link id 24247: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24247: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24247: 0.00019216537475586 --> \n<tr><td><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/Wise2\/index.html\" id=\"link-23768\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Genewise<\/a>\n<!-- Time to render name section of link id 23768: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Wise2 is a package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence.<\/p>\n<!-- Time to render link large description section of link id 23768: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Genewise> How to use <\/a>\n<!-- Time to render notes section of link id 23768: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23768: 0.00018215179443359 --> \n<tr><td><a href=\"https:\/\/github.com\/cpockrandt\/genmap\" id=\"link-25923\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenMap<\/a>\n<!-- Time to render name section of link id 25923: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast and Exact Computation of Genome Mappability.<\/p>\n<!-- Time to render link large description section of link id 25923: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenMap> How to use <\/a>\n<!-- Time to render notes section of link id 25923: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25923: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/danny-wilson\/genomegaMap\" id=\"link-25340\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">genomegaMap<\/a>\n<!-- Time to render name section of link id 25340: 2.1457672119141E-6 --> \n<\/td>\n<td>Within-species genome-wide dN\/dS estimation from very many genomes.\n<!-- Time to render link large description section of link id 25340: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_genomegaMap> How to use <\/a>\n<!-- Time to render notes section of link id 25340: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25340: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/schatzlab\/genomescope\" id=\"link-24072\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeScope<\/a>\n<!-- Time to render name section of link id 24072: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Fast genome analysis from unassembled short reads<\/p>\n<!-- Time to render link large description section of link id 24072: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeScope> How to use <\/a>\n<!-- Time to render notes section of link id 24072: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24072: 0.00016880035400391 --> \n<tr><td><a href=\"https:\/\/github.com\/tbenavi1\/genomescope2.0\" id=\"link-24248\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeScope2.0<\/a>\n<!-- Time to render name section of link id 24248: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Reference-free profiling of polyploid genomes<\/p>\n<!-- Time to render link large description section of link id 24248: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeScope2.0> How to use <\/a>\n<!-- Time to render notes section of link id 24248: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24248: 0.00017094612121582 --> \n<tr><td><a href=\"http:\/\/software.broadinstitute.org\/software\/genomestrip\/\" id=\"link-23817\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeSTRiP<\/a>\n<!-- Time to render name section of link id 23817: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.<\/p>\n<!-- Time to render link large description section of link id 23817: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23817: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23817: 0.00018596649169922 --> \n<tr><td><a href=\"http:\/\/genomethreader.org\/\" id=\"link-23887\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeThreader<\/a>\n<!-- Time to render name section of link id 23887: 2.8610229492188E-6 --> \n<\/td>\n<td><p>GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA\/EST and\/or protein sequences are used to predict gene structures via spliced alignments.<\/p>\n<!-- Time to render link large description section of link id 23887: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeThreader> How to use <\/a>\n<!-- Time to render notes section of link id 23887: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23887: 0.00019311904907227 --> \n<tr><td><a href=\"http:\/\/genometools.org\/index.html\" id=\"link-23637\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeTools<\/a>\n<!-- Time to render name section of link id 23637: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named \"gt\".<\/p>\n<!-- Time to render link large description section of link id 23637: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeTools> How to use <\/a>\n<!-- Time to render notes section of link id 23637: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23637: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/seqoccin\/GenomOrder\" id=\"link-24249\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomOrder<\/a>\n<!-- Time to render name section of link id 24249: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GenomOrder is a Nextflow pipeline reordering and renaming scaffolds from up to 5 assemblies using a reference. It is also able to produce D-Genies back-up files allowing rapid visual comparison of chromosomes of the assemblies versus the reference. These files can be uploaded and visualized with the online tool D-Genies : http:\/\/dgenies.toulouse.inra.fr\/ The assembly mapping versus the reference is performed with minimap2. These assemblies can be scaffolded or not. If they are not, an option enables to scaffold them according to the reference. The pipeline produces D-Genies back-up file for a user defined list of reference chromosomes. The chromosome file contains one reference chromosome name per line.<\/p>\n<!-- Time to render link large description section of link id 24249: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24249: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24249: 0.00017213821411133 --> \n<tr><td><a href=\"https:\/\/github.com\/uni-halle\/gerbil\" id=\"link-24250\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gerbil<\/a>\n<!-- Time to render name section of link id 24250: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A basic task in bioinformatics is the counting of k-mers in genome strings.<\/p>\n<!-- Time to render link large description section of link id 24250: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24250: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24250: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/pkalbers\/geva\" id=\"link-24252\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEVA<\/a>\n<!-- Time to render name section of link id 24252: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Genealogical Estimation of Variant Age. We have developed a method for estimating the age of genetic variants; that is, the time of origin of an allele through mutation at a single locus. Our approach, which we refer to as the Genealogical Estimation of Variant Age (GEVA), is similar to existing methods that involve coalescent modeling to infer the time to the most recent common ancestor (TMRCA) between individual genomes <13, 23, 24>. However, these methods typically operate on a discretized timescale <13>, utilize only a fraction of the information available in larger sample data <25>, or employ approximations to overcome computational complexity <14, 15, 26>.<\/p>\n<!-- Time to render link large description section of link id 24252: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24252: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24252: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/marschall-lab\/GFAffix\" id=\"link-25428\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GFAffix<\/a>\n<!-- Time to render name section of link id 25428: 3.0994415283203E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25428: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GFAffix> How to use <\/a>\n<!-- Time to render notes section of link id 25428: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25428: 0.00019717216491699 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/gfatools\" id=\"link-24254\" class=\"track_this_link \" rel=\"noopener noreferrer\">gfatools<\/a>\n<!-- Time to render name section of link id 24254: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA\/BED.<\/p>\n<!-- Time to render link large description section of link id 24254: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gfatools> How to use <\/a>\n<!-- Time to render notes section of link id 24254: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24254: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/ggonnella\/gfaviz\" id=\"link-25600\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GfaViz<\/a>\n<!-- Time to render name section of link id 25600: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Graphical interactive tool for the visualization of sequence graphs in GFA format.<\/p>\n<!-- Time to render link large description section of link id 25600: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GfaViz> How to use <\/a>\n<!-- Time to render notes section of link id 25600: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25600: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/billzt\/gff3sort\" id=\"link-24255\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gff3sort<\/a>\n<!-- Time to render name section of link id 24255: 9.1075897216797E-5 --> \n<\/td>\n<td><p>A Perl Script to sort gff3 files and produce suitable results for tabix tools<\/p>\n<!-- Time to render link large description section of link id 24255: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24255: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24255: 0.0002591609954834 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-pathogens\/gff3toembl\" id=\"link-23929\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gff3toembl<\/a>\n<!-- Time to render name section of link id 23929: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI<\/p>\n<!-- Time to render link large description section of link id 23929: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23929: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23929: 0.0001680850982666 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/gffcompare\" id=\"link-24256\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gffcompare<\/a>\n<!-- Time to render name section of link id 24256: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the \u201cquery\u201d files), when compared with a reference annotation (also provided as GFF).<\/p>\n<!-- Time to render link large description section of link id 24256: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gffcompare> How to use <\/a>\n<!-- Time to render notes section of link id 24256: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24256: 0.0001671314239502 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/gffread\" id=\"link-24066\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gffread<\/a>\n<!-- Time to render name section of link id 24066: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GFF\/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.<\/p>\n<!-- Time to render link large description section of link id 24066: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gffread> How to use <\/a>\n<!-- Time to render notes section of link id 24066: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24066: 0.0001678466796875 --> \n<tr><td><a href=\"https:\/\/github.com\/bacpop\/ggCaller\" id=\"link-25574\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ggCaller<\/a>\n<!-- Time to render name section of link id 25574: 2.8610229492188E-6 --> \n<\/td>\n<td>A de Bruijn graph-based gene-caller and pangenome analysis tool.\n<!-- Time to render link large description section of link id 25574: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ggCaller> How to use <\/a>\n<!-- Time to render notes section of link id 25574: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25574: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/pachterlab\/gget\" id=\"link-24689\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gget<\/a>\n<!-- Time to render name section of link id 24689: 2.8610229492188E-6 --> \n<\/td>\n<td><p>gget enables efficient querying of genomic reference databases.<\/p>\n<!-- Time to render link large description section of link id 24689: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24689: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24689: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/cli\/cli\" id=\"link-24257\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gh-cli<\/a>\n<!-- Time to render name section of link id 24257: 1.9073486328125E-6 --> \n<\/td>\n<td><p>gh is GitHub on the command line. It brings pull requests, issues, and other GitHub concepts to the terminal next to where you are already working with git and your code.<\/p>\n<!-- Time to render link large description section of link id 24257: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24257: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24257: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/www.haskell.org\/ghc\/\" id=\"link-24111\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GHC<\/a>\n<!-- Time to render name section of link id 24111: 3.0994415283203E-6 --> \n<\/td>\n<td><p>GHC is a state-of-the-art, open source, compiler and interactive environment for the functional language Haskell<\/p>\n<!-- Time to render link large description section of link id 24111: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24111: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24111: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/DRL\/gIMble\" id=\"link-24102\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gIMble<\/a>\n<!-- Time to render name section of link id 24102: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A genome-wide IM blockwise likelihood estimation toolkit<\/p>\n<!-- Time to render link large description section of link id 24102: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24102: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24102: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/i10labtitech\/GINGER\" id=\"link-25803\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GINGER<\/a>\n<!-- Time to render name section of link id 25803: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GINGER is a tool that is implemented an integrated method for gene structure prediction in higher eukaryotes.<\/p>\n<!-- Time to render link large description section of link id 25803: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GINGER> How to use <\/a>\n<!-- Time to render notes section of link id 25803: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25803: 0.00016379356384277 --> \n<tr><td><a href=\"https:\/\/ccb.jhu.edu\/software\/glimmerhmm\/\" id=\"link-25512\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GlimmerHMM<\/a>\n<!-- Time to render name section of link id 25512: 3.0994415283203E-6 --> \n<\/td>\n<td><p>GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).<\/p>\n<!-- Time to render link large description section of link id 25512: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GlimmerHMM> How to use <\/a>\n<!-- Time to render notes section of link id 25512: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25512: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/odelaneau.github.io\/GLIMPSE\/index.html\" id=\"link-24258\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GLIMPSE<\/a>\n<!-- Time to render name section of link id 24258: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.<\/p>\n<!-- Time to render link large description section of link id 24258: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GLIMPSE> How to use <\/a>\n<!-- Time to render notes section of link id 24258: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24258: 0.00017309188842773 --> \n<tr><td><a href=\"http:\/\/research-pub.gene.com\/gmap\/\" id=\"link-23638\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GMAP-GSNAP<\/a>\n<!-- Time to render name section of link id 23638: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GMAP: A Genomic Mapping and Alignment Program for mRNA and EST SequencesGSNAP: Genomic Short-read Nucleotide Alignment Program<\/p>\n<!-- Time to render link large description section of link id 23638: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GMAP-GSNAP> How to use <\/a>\n<!-- Time to render notes section of link id 23638: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23638: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/www.genoscope.cns.fr\/externe\/gmove\/\" id=\"link-23800\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gmove<\/a>\n<!-- Time to render name section of link id 23800: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Gmove is a genome annotation tool. This combiner takes as input mapping of RNA-seq or protein or ab initio data.<\/p>\n<!-- Time to render link large description section of link id 23800: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23800: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23800: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/evolbioinfo\/goalign\" id=\"link-24259\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Goalign<\/a>\n<!-- Time to render name section of link id 24259: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Goalign is a set of command line tools to manipulate multiple alignments.<\/p>\n<!-- Time to render link large description section of link id 24259: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Goalign> How to use <\/a>\n<!-- Time to render notes section of link id 24259: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24259: 0.00019311904907227 --> \n<tr><td><a href=\"https:\/\/github.com\/tanghaibao\/goatools\" id=\"link-25258\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">goatools<\/a>\n<!-- Time to render name section of link id 25258: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Python library to handle Gene Ontology (GO) terms.<\/p>\n<!-- Time to render link large description section of link id 25258: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_goatools> How to use <\/a>\n<!-- Time to render notes section of link id 25258: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25258: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/esrud\/GONE\" id=\"link-25444\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GONE<\/a>\n<!-- Time to render name section of link id 25444: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This program calculates and uses linkage disequilibrium at genomic marker loci to infer the effective population size trajectories over a period of about 100-200 hundred generations back in time.<\/p>\n<!-- Time to render link large description section of link id 25444: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GONE> How to use <\/a>\n<!-- Time to render notes section of link id 25444: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25444: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/evolbioinfo\/gotree\" id=\"link-25525\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gotree<\/a>\n<!-- Time to render name section of link id 25525: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Gotree is a set of command line tools and an API to manipulate phylogenetic trees.<\/p>\n<!-- Time to render link large description section of link id 25525: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gotree> How to use <\/a>\n<!-- Time to render notes section of link id 25525: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25525: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/gradle.org\" id=\"link-26020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gradle<\/a>\n<!-- Time to render name section of link id 26020: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Gradle is the open source build system of choice for Java, Android, and Kotlin developers.<\/p>\n<!-- Time to render link large description section of link id 26020: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gradle> How to use <\/a>\n<!-- Time to render notes section of link id 26020: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26020: 0.00017213821411133 --> \n<tr><td><a href=\"https:\/\/github.com\/cgroza\/GraffiTE\" id=\"link-25334\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraffiTE<\/a>\n<!-- Time to render name section of link id 25334: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and\/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.<\/p>\n<!-- Time to render link large description section of link id 25334: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GraffiTE> How to use <\/a>\n<!-- Time to render notes section of link id 25334: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25334: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/forge.ird.fr\/diade\/dynadiv\/grannot\" id=\"link-25728\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GrAnnoT<\/a>\n<!-- Time to render name section of link id 25728: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GrAnnoT is an annotation transfer tool for pangenome graphs.<\/p>\n<!-- Time to render link large description section of link id 25728: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GrAnnoT> How to use <\/a>\n<!-- Time to render notes section of link id 25728: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25728: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/maickrau\/GraphAligner\" id=\"link-24261\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphAligner<\/a>\n<!-- Time to render name section of link id 24261: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Seed-and-extend program for aligning long error-prone reads to genome graphs.<\/p>\n<!-- Time to render link large description section of link id 24261: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GraphAligner> How to use <\/a>\n<!-- Time to render notes section of link id 24261: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24261: 0.00059199333190918 --> \n<tr><td><a href=\"http:\/\/huttenhower.sph.harvard.edu\/GraPhlAn\" id=\"link-23837\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraPhlAn<\/a>\n<!-- Time to render name section of link id 23837: 7.1525573730469E-6 --> \n<\/td>\n<td><p>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.<\/p>\n<!-- Time to render link large description section of link id 23837: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23837: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23837: 0.00053191184997559 --> \n<tr><td><a href=\"https:\/\/github.com\/isovic\/graphmap\" id=\"link-24262\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphMap<\/a>\n<!-- Time to render name section of link id 24262: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A highly sensitive and accurate mapper for long, error-prone reads.<\/p>\n<!-- Time to render link large description section of link id 24262: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24262: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24262: 0.00050687789916992 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/graphtyper\" id=\"link-24263\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">graphtyper<\/a>\n<!-- Time to render name section of link id 24263: 7.1525573730469E-6 --> \n<\/td>\n<td><p>graphtyper is a graph-based variant caller capable of genotyping population-scale short read data sets.<\/p>\n<!-- Time to render link large description section of link id 24263: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_graphtyper> How to use <\/a>\n<!-- Time to render notes section of link id 24263: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24263: 0.00050497055053711 --> \n<tr><td><a href=\"https:\/\/github.com\/nadegeguiglielmoni\/GraphUnzip\" id=\"link-24702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphUnzip<\/a>\n<!-- Time to render name section of link id 24702: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Unzip assembly graphs with Hi-C data and\/or long reads.<\/p>\n<!-- Time to render link large description section of link id 24702: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24702: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24702: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/lczech\/grenedalf\" id=\"link-25863\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">grenedalf<\/a>\n<!-- Time to render name section of link id 25863: 1.9073486328125E-6 --> \n<\/td>\n<td><p>grenedalf is a collection of commands for working with pool sequencing population genetic data.<\/p>\n<!-- Time to render link large description section of link id 25863: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_grenedalf> How to use <\/a>\n<!-- Time to render notes section of link id 25863: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25863: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/PapenfussLab\/gridss\" id=\"link-24264\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GRIDSS<\/a>\n<!-- Time to render name section of link id 24264: 3.0994415283203E-6 --> \n<\/td>\n<td><p>GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.<\/p>\n<!-- Time to render link large description section of link id 24264: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GRIDSS> How to use <\/a>\n<!-- Time to render notes section of link id 24264: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24264: 0.00041508674621582 --> \n<tr><td><a href=\"http:\/\/sourceforge.net\/projects\/biogrinder\/\" id=\"link-23639\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Grinder<\/a>\n<!-- Time to render name section of link id 23639: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.<\/p>\n<!-- Time to render link large description section of link id 23639: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23639: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23639: 0.00023508071899414 --> \n<tr><td><a href=\"http:\/\/www.gromacs.org\/About_Gromacs\" id=\"link-23876\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GROMACS<\/a>\n<!-- Time to render name section of link id 23876: 4.0531158447266E-6 --> \n<\/td>\n<td><p>GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.<\/p>\n<!-- Time to render link large description section of link id 23876: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GROMACS> How to use <\/a>\n<!-- Time to render notes section of link id 23876: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23876: 0.0002138614654541 --> \n<tr><td><a href=\"https:\/\/github.com\/hsinnan75\/GSAlign\" id=\"link-24265\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GSAlign<\/a>\n<!-- Time to render name section of link id 24265: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An ultra-fast sequence alignment algorithm for intra-species genome comparison.<\/p>\n<!-- Time to render link large description section of link id 24265: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GSAlign> How to use <\/a>\n<!-- Time to render notes section of link id 24265: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24265: 0.0002140998840332 --> \n<tr><td><a href=\"https:\/\/ecogenomics.github.io\/GTDBTk\/\" id=\"link-24266\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GTDB-Tk<\/a>\n<!-- Time to render name section of link id 24266: 2.8610229492188E-6 --> \n<\/td>\n<td><p>GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.<\/p>\n<!-- Time to render link large description section of link id 24266: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GTDB-Tk> How to use <\/a>\n<!-- Time to render notes section of link id 24266: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24266: 0.00021505355834961 --> \n<tr><td><a href=\"http:\/\/www.genemine.org\/gtftools.php\" id=\"link-24267\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GTFtools<\/a>\n<!-- Time to render name section of link id 24267: 4.0531158447266E-6 --> \n<\/td>\n<td><p>GTFtools provides a set of functions to analyze various modes of gene models.<\/p>\n<!-- Time to render link large description section of link id 24267: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GTFtools> How to use <\/a>\n<!-- Time to render notes section of link id 24267: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24267: 0.00023603439331055 --> \n<tr><td><a href=\"http:\/\/www.well.ox.ac.uk\/~cfreeman\/software\/gwas\/gtool.html\" id=\"link-23792\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gtools<\/a>\n<!-- Time to render name section of link id 23792: 2.8610229492188E-6 --> \n<\/td>\n<td><p>GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.<\/p>\n<!-- Time to render link large description section of link id 23792: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23792: 0.00048518180847168 --> \n<\/td><\/tr>\n<!-- Time to render link id 23792: 0.0007178783416748 --> \n<tr><td><a href=\"https:\/\/github.com\/nickjcroucher\/gubbins\" id=\"link-24268\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gubbins<\/a>\n<!-- Time to render name section of link id 24268: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.<\/p>\n<!-- Time to render link large description section of link id 24268: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gubbins> How to use <\/a>\n<!-- Time to render notes section of link id 24268: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24268: 0.00021505355834961 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/hal2vg\" id=\"link-25449\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hal2vg<\/a>\n<!-- Time to render name section of link id 25449: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Convert HAL to vg-compatible sequence graph.<\/p>\n<!-- Time to render link large description section of link id 25449: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hal2vg> How to use <\/a>\n<!-- Time to render notes section of link id 25449: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25449: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/HMPNK\/HANNO\" id=\"link-25535\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HANNO<\/a>\n<!-- Time to render name section of link id 25535: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Efficient High-throughput ANNOtation of protein coding genes in eukaryote genomes.<\/p>\n<!-- Time to render link large description section of link id 25535: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HANNO> How to use <\/a>\n<!-- Time to render notes section of link id 25535: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25535: 0.00021505355834961 --> \n<tr><td><a href=\"https:\/\/github.com\/browning-lab\/hap-ibd\" id=\"link-25149\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hap-ibd<\/a>\n<!-- Time to render name section of link id 25149: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.<\/p>\n<!-- Time to render link large description section of link id 25149: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hap-ibd> How to use <\/a>\n<!-- Time to render notes section of link id 25149: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25149: 0.00021505355834961 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/hap.py\" id=\"link-25190\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hap.py<\/a>\n<!-- Time to render name section of link id 25190: 1.9073486328125E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25190: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hap.py> How to use <\/a>\n<!-- Time to render notes section of link id 25190: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25190: 0.0002129077911377 --> \n<tr><td><a href=\"https:\/\/github.com\/smajidian\/Hap10\" id=\"link-24270\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hap10<\/a>\n<!-- Time to render name section of link id 24270: 3.814697265625E-6 --> \n<\/td>\n<td><p>The goal is to reconstruct accurate and long haplotypes polyploid genome using linked reads.<\/p>\n<!-- Time to render link large description section of link id 24270: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24270: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24270: 0.00022697448730469 --> \n<tr><td><a href=\"https:\/\/github.com\/vibansal\/HapCUT2\" id=\"link-23841\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HapCUT2<\/a>\n<!-- Time to render name section of link id 23841: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Software tools for haplotype assembly from sequence data<\/p>\n<!-- Time to render link large description section of link id 23841: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HapCUT2> How to use <\/a>\n<!-- Time to render notes section of link id 23841: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23841: 0.0002140998840332 --> \n<tr><td><a href=\"https:\/\/forge-dga.jouy.inra.fr\/projects\/hapflk\/\" id=\"link-23640\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hapflk<\/a>\n<!-- Time to render name section of link id 23640: 1.9073486328125E-6 --> \n<\/td>\n<td><p>hapflk is a software implementing the hapFLK <1> and FLK <2> tests for the detection of selection signatures based on multiple population genotyping data.<\/p>\n<!-- Time to render link large description section of link id 23640: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hapflk> How to use <\/a>\n<!-- Time to render notes section of link id 23640: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23640: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/zengxiaofei\/HapHiC\" id=\"link-26013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HapHiC<\/a>\n<!-- Time to render name section of link id 26013: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HapHiC is an allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules.<\/p>\n<!-- Time to render link large description section of link id 26013: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HapHiC> How to use <\/a>\n<!-- Time to render notes section of link id 26013: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26013: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/gwcbi\/haphpipe\" id=\"link-25171\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HAPHPIPE<\/a>\n<!-- Time to render name section of link id 25171: 2.8610229492188E-6 --> \n<\/td>\n<td><p>NGS viral assembly and population genetics.<\/p>\n<!-- Time to render link large description section of link id 25171: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HAPHPIPE> How to use <\/a>\n<!-- Time to render notes section of link id 25171: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25171: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/seppinho\/haplogrep-cmd\" id=\"link-24271\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haplogrep<\/a>\n<!-- Time to render name section of link id 24271: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Haplogrep is a command-line tool for mtDNA haplogroup classification.<\/p>\n<!-- Time to render link large description section of link id 24271: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24271: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24271: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/Nobel-Justin\/HaploHiC\" id=\"link-24272\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HaploHiC<\/a>\n<!-- Time to render name section of link id 24272: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Comprehensive haplotype division of Hi-C PE-reads based on local contacts ratio.<\/p>\n<!-- Time to render link large description section of link id 24272: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24272: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24272: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/mapleforest\/HaploMerger2\" id=\"link-23846\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HaploMerger2<\/a>\n<!-- Time to render name section of link id 23846: 3.0994415283203E-6 --> \n<\/td>\n<td><p>&lt;HaploMerger2 (HM2) is an important upgrade over HaploMerger. HM2 is an easy-to-use automated pipeline for improving genome assembly in the post-assembly stage. It consists of a set of executables as well as wrappers for several third-part software.<\/p>\n<!-- Time to render link large description section of link id 23846: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23846: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23846: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/dmarnetto\/haplostrips\/src\/master\/\" id=\"link-25020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haplostrips<\/a>\n<!-- Time to render name section of link id 25020: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Haplostrips produce plots that depict variants in a genomic window among different samples. Visualize similarities between haplotypes with respect to a reference haplotype through haplotype clustering and sorting, useful for revealing hidden population structure.<\/p>\n<!-- Time to render link large description section of link id 25020: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Haplostrips> How to use <\/a>\n<!-- Time to render notes section of link id 25020: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25020: 0.00020408630371094 --> \n<tr><td><a href=\"https:\/\/www.broadinstitute.org\/haploview\/haploview\" id=\"link-24273\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haploview<\/a>\n<!-- Time to render name section of link id 24273: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.<\/p>\n<!-- Time to render link large description section of link id 24273: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24273: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24273: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/institut-de-genomique\/HAPO-G\" id=\"link-24274\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hapo-G<\/a>\n<!-- Time to render name section of link id 24274: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.<\/p>\n<!-- Time to render link large description section of link id 24274: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hapo-G> How to use <\/a>\n<!-- Time to render notes section of link id 24274: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24274: 0.00016379356384277 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/harvest-tools\" id=\"link-25350\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HarvestTools<\/a>\n<!-- Time to render name section of link id 25350: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HarvestTools is a utility for creating and interfacing with Gingr files, which are efficient archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.<\/p>\n<!-- Time to render link large description section of link id 25350: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HarvestTools> How to use <\/a>\n<!-- Time to render notes section of link id 25350: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25350: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/vpc-ccg\/haslr\" id=\"link-24275\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HASLR<\/a>\n<!-- Time to render name section of link id 24275: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.<\/p>\n<!-- Time to render link large description section of link id 24275: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24275: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24275: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/AbeelLab\/hat\" id=\"link-24276\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HAT-phasing<\/a>\n<!-- Time to render name section of link id 24276: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HAT is a haplotype assembly tool that use NGS and TGS data along a reference genome to reconstruct haplotypes.<\/p>\n<!-- Time to render link large description section of link id 24276: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24276: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24276: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/SegataLab\/hclust2\" id=\"link-25526\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hclust2<\/a>\n<!-- Time to render name section of link id 25526: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.<\/p>\n<!-- Time to render link large description section of link id 25526: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hclust2> How to use <\/a>\n<!-- Time to render notes section of link id 25526: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25526: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/bioconda.github.io\/recipes\/hcluster_sg\/README.html\" id=\"link-23842\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hcluster_sg<\/a>\n<!-- Time to render name section of link id 23842: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A hierarchical clustering software for sparse graphs<\/p>\n<!-- Time to render link large description section of link id 23842: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23842: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23842: 0.00018811225891113 --> \n<tr><td><a href=\"https:\/\/portal.hdfgroup.org\/display\/HDFVIEW\/HDFView\" id=\"link-24050\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HDFView<\/a>\n<!-- Time to render name section of link id 24050: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HDFView is a visual tool for browsing and editing HDF4 and HDF5 files.<\/p>\n<!-- Time to render link large description section of link id 24050: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24050: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24050: 0.00021195411682129 --> \n<tr><td><a href=\"https:\/\/github.com\/NDBL\/HECIL\" id=\"link-24033\" class=\"track_this_link \" rel=\"noopener noreferrer\">HECIL<\/a>\n<!-- Time to render name section of link id 24033: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Hybrid Error Correction of Long Reads using Iterative Learning<\/p>\n<!-- Time to render link large description section of link id 24033: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24033: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24033: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/kishwarshafin\/helen\" id=\"link-24284\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HELEN<\/a>\n<!-- Time to render name section of link id 24284: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HELEN (Homopolymer Encoded Long-read Error-corrector for Nanopore) uses a Recurrent-Neural-Network (RNN) based Multi-Task Learning (MTL) model that can predict a base and a run-length for each genomic position using the weights generated by MarginPolish. This installation includes MarginPolish.<\/p>\n<!-- Time to render link large description section of link id 24284: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24284: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24284: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/richarddurbin\/hexamer\" id=\"link-25443\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hexamer<\/a>\n<!-- Time to render name section of link id 25443: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Find likely coding segments in DNA using composition-normalised hexamer tables.<\/p>\n<!-- Time to render link large description section of link id 25443: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hexamer> How to use <\/a>\n<!-- Time to render notes section of link id 25443: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25443: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/HG-CoLoR\" id=\"link-24044\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HG-CoLoR<\/a>\n<!-- Time to render name section of link id 24044: 3.0994415283203E-6 --> \n<\/td>\n<td><p>HG-CoLoR (Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads) is a hybrid method for the error correction of long reads that both aligns the short reads to the long reads, and uses a variable-order de Bruijn graph, in a seed-and-extend approach.<\/p>\n<!-- Time to render link large description section of link id 24044: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24044: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24044: 0.00017809867858887 --> \n<tr><td><a href=\"http:\/\/kalarikrlab.org\/Software\/HGT-ID.html\" id=\"link-24104\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HGT-ID<\/a>\n<!-- Time to render name section of link id 24104: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An efficient and sensitive program for detecting viral insertion sequences from known viral reference genome in the genome of human cancers.<\/p>\n<!-- Time to render link large description section of link id 24104: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24104: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24104: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/qiyunlab\/HGTector\" id=\"link-24285\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HGTector<\/a>\n<!-- Time to render name section of link id 24285: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.<\/p>\n<!-- Time to render link large description section of link id 24285: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24285: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24285: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/maxplanck-ie\/HiCAssembler\" id=\"link-25725\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HiCAssembler<\/a>\n<!-- Time to render name section of link id 25725: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software to assemble contigs\/scaffolds into chromosomes using Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 25725: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiCAssembler> How to use <\/a>\n<!-- Time to render notes section of link id 25725: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25725: 0.00019598007202148 --> \n<tr><td><a href=\"https:\/\/hicexplorer.readthedocs.io\/en\/latest\/index.html\" id=\"link-24287\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HiCExplorer<\/a>\n<!-- Time to render name section of link id 24287: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 24287: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiCExplorer> How to use <\/a>\n<!-- Time to render notes section of link id 24287: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24287: 0.00018811225891113 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/hickit\" id=\"link-25032\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hickit<\/a>\n<!-- Time to render name section of link id 25032: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Hickit is a set of tools initially developed to process diploid single-cell Hi-C data. It extracts contact pairs from read alignment, identifies phases of contacts overlapping with SNPs of known phases, imputes missing phases, infers the 3D structure of a single cell and visualizes the structure.<\/p>\n<!-- Time to render link large description section of link id 25032: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hickit> How to use <\/a>\n<!-- Time to render notes section of link id 25032: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25032: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/XiaoTaoWang\/HiCLift\" id=\"link-24709\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HiCLift<\/a>\n<!-- Time to render name section of link id 24709: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and efficient tool for converting chromatin interaction data between genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24709: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24709: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24709: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/sheinasim\/HiFiAdapterFilt\" id=\"link-24291\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HiFiAdapterFilt<\/a>\n<!-- Time to render name section of link id 24291: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences.<\/p>\n<!-- Time to render link large description section of link id 24291: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiFiAdapterFilt> How to use <\/a>\n<!-- Time to render notes section of link id 24291: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24291: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/chhylp123\/hifiasm\" id=\"link-24292\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\">hifiasm<\/a>\n<!-- Time to render name section of link id 24292: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome.<\/p>\n<!-- Time to render link large description section of link id 24292: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hifiasm> How to use <\/a>\n<!-- Time to render notes section of link id 24292: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24292: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/xfengnefx\/hifiasm-meta\" id=\"link-24293\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\">hifiasm-meta<\/a>\n<!-- Time to render name section of link id 24293: 2.8610229492188E-6 --> \n<\/td>\n<td><p>De novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.<\/p>\n<!-- Time to render link large description section of link id 24293: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hifiasm-meta> How to use <\/a>\n<!-- Time to render notes section of link id 24293: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24293: 0.00019311904907227 --> \n<tr><td><a href=\"https:\/\/daehwankimlab.github.io\/hisat2\/\" id=\"link-23921\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HISAT2<\/a>\n<!-- Time to render name section of link id 23921: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).<\/p>\n<!-- Time to render link large description section of link id 23921: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HISAT2> How to use <\/a>\n<!-- Time to render notes section of link id 23921: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23921: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/hmmer.org\/\" id=\"link-23642\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HMMER<\/a>\n<!-- Time to render name section of link id 23642: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HMMER is a package used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).<\/p>\n<!-- Time to render link large description section of link id 23642: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HMMER> How to use <\/a>\n<!-- Time to render notes section of link id 23642: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23642: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/homer.ucsd.edu\/homer\/\" id=\"link-23643\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Homer<\/a>\n<!-- Time to render name section of link id 23643: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.\u00a0 It is a collection of command line programs for unix-style operating systems written in Perl and C++.<\/p>\n<!-- Time to render link large description section of link id 23643: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HOMER> How to use <\/a>\n<!-- Time to render notes section of link id 23643: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23643: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/cmbi\/hssp\" id=\"link-25667\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hssp<\/a>\n<!-- Time to render name section of link id 25667: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Create DSSP and HSSP files. A series of PDB-related databanks for everyday needs.<\/p>\n<!-- Time to render link large description section of link id 25667: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hssp> How to use <\/a>\n<!-- Time to render notes section of link id 25667: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25667: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/www-huber.embl.de\/users\/anders\/HTSeq\/doc\/overview.html\" id=\"link-23644\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HTSeq<\/a>\n<!-- Time to render name section of link id 23644: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.<\/p>\n<!-- Time to render link large description section of link id 23644: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HTSeq> How to use <\/a>\n<!-- Time to render notes section of link id 23644: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23644: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/huttenhower.sph.harvard.edu\/humann\/\" id=\"link-24911\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HUMAnN<\/a>\n<!-- Time to render name section of link id 24911: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HUMAnN is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24911: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HUMAnN> How to use <\/a>\n<!-- Time to render notes section of link id 24911: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24911: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/hyphy.org\/\" id=\"link-23645\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HyPhy<\/a>\n<!-- Time to render name section of link id 23645: 3.0994415283203E-6 --> \n<\/td>\n<td><p>HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses.<\/p>\n<!-- Time to render link large description section of link id 23645: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HyPhy> How to use <\/a>\n<!-- Time to render notes section of link id 23645: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23645: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/kensung-lab\/hypo\" id=\"link-24298\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HyPO<\/a>\n<!-- Time to render name section of link id 24298: 3.814697265625E-6 --> \n<\/td>\n<td><p>HyPo (a Hybrid Polisher): Super Fast &amp; Accurate Polisher for Long Read Genome Assemblies<\/p>\n<!-- Time to render link large description section of link id 24298: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HyPo> How to use <\/a>\n<!-- Time to render notes section of link id 24298: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24298: 0.00018787384033203 --> \n<tr><td><a href=\"https:\/\/github.com\/VIB-PSB\/i-ADHoRe\" id=\"link-24994\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">i-ADHoRe<\/a>\n<!-- Time to render name section of link id 24994: 3.0994415283203E-6 --> \n<\/td>\n<td><p>i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.<\/p>\n<!-- Time to render link large description section of link id 24994: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_i-ADHoRe> How to use <\/a>\n<!-- Time to render notes section of link id 24994: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24994: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0020\" id=\"link-24747\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IBA<\/a>\n<!-- Time to render name section of link id 24747: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Python script to assemble AHE (Anchored Hybrid Enrichment) data loci by loci. To summarize, raw sequencing reads for each species were filtered for quality using Trim Galore! v. 0.4.0 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b9005\" name=\"bb9005\"><span class=\"anchor-text\">Krueger, 2015<\/span><\/a>), and assembled using the iterative baited assembly (IBA) Python script which employs USEARCH v. 7.0 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0060\" name=\"bb0060\"><span class=\"anchor-text\">Edgar, 2010<\/span><\/a>) and Bridger v. 2014-12-01 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0030\" name=\"bb0030\"><span class=\"anchor-text\">Chang et al., 2015<\/span><\/a>) to assemble loci for each taxon. MAFFT v. 7.245 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0160\" name=\"bb0160\"><span class=\"anchor-text\">Katoh and Standley, 2013<\/span><\/a>) was used to align assembled sequences, and the probe and\u00a0<a class=\"topic-link\" title=\"Learn more about flanking regions from ScienceDirect's AI-generated Topic Pages\" href=\"https:\/\/www.sciencedirect.com\/topics\/biochemistry-genetics-and-molecular-biology\/dna-flanking-region\">flanking regions<\/a>\u00a0were separated with the Python script Extract_probe_region.py (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0020\" name=\"bb0020\"><span class=\"anchor-text\">Breinholt et al., 2018<\/span><\/a>).<\/p>\n<!-- Time to render link large description section of link id 24747: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24747: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24747: 0.0003821849822998 --> \n<tr><td><a href=\"https:\/\/icescreen.migale.inrae.fr\" id=\"link-25280\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ICEscreen<\/a>\n<!-- Time to render name section of link id 25280: 8.1062316894531E-6 --> \n<\/td>\n<td><p>ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes.<\/p>\n<!-- Time to render link large description section of link id 25280: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ICEscreen> How to use <\/a>\n<!-- Time to render notes section of link id 25280: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25280: 0.00053501129150391 --> \n<tr><td><a href=\"https:\/\/github.com\/kundajelab\/idr\" id=\"link-24691\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IDR<\/a>\n<!-- Time to render name section of link id 24691: 8.1062316894531E-6 --> \n<\/td>\n<td><p>The IDR (Irreproducible Discovery Rate) framework is a uni\ufb01ed approach to measure the reproducibility of \ufb01ndings identi\ufb01ed from replicate experiments and provide highly stable thresholds based on reproducibility.<\/p>\n<!-- Time to render link large description section of link id 24691: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IDR> How to use <\/a>\n<!-- Time to render notes section of link id 24691: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24691: 0.00052499771118164 --> \n<tr><td><a href=\"http:\/\/www.broadinstitute.org\/software\/igv\/home\" id=\"link-23647\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">IGV<\/a>\n<!-- Time to render name section of link id 23647: 8.1062316894531E-6 --> \n<\/td>\n<td><p>The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.<\/p>\n<!-- Time to render link large description section of link id 23647: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IGV> How to use <\/a>\n<!-- Time to render notes section of link id 23647: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23647: 0.00054192543029785 --> \n<tr><td><a href=\"https:\/\/jmarchini.org\/software\/#impute-5\" id=\"link-23769\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">IMPUTE5<\/a>\n<!-- Time to render name section of link id 23769: 3.814697265625E-6 --> \n<\/td>\n<td><p>IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples.<\/p>\n<!-- Time to render link large description section of link id 23769: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IMPUTE5> How to use <\/a>\n<!-- Time to render notes section of link id 23769: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23769: 0.00030398368835449 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/infernal\/\" id=\"link-23648\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Infernal<\/a>\n<!-- Time to render name section of link id 23648: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).<\/p>\n<!-- Time to render link large description section of link id 23648: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Infernal> How to use <\/a>\n<!-- Time to render notes section of link id 23648: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23648: 0.00029706954956055 --> \n<tr><td><a href=\"https:\/\/github.com\/mapequation\/infomap\" id=\"link-24833\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Infomap<\/a>\n<!-- Time to render name section of link id 24833: 3.814697265625E-6 --> \n<\/td>\n<td><p>Multi-level network clustering based on the Map Equation.<\/p>\n<!-- Time to render link large description section of link id 24833: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24833: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24833: 0.00030994415283203 --> \n<tr><td><a href=\"https:\/\/github.com\/HadrienG\/InSilicoSeq\" id=\"link-25786\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">InSilicoSeq<\/a>\n<!-- Time to render name section of link id 25786: 3.814697265625E-6 --> \n<\/td>\n<td><p>InSilicoSeq is a sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.<\/p>\n<!-- Time to render link large description section of link id 25786: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_InSilicoSeq> How to use <\/a>\n<!-- Time to render notes section of link id 25786: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25786: 0.00032401084899902 --> \n<tr><td><a href=\"https:\/\/github.com\/ChongLab\/Inspector\" id=\"link-24299\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Inspector<\/a>\n<!-- Time to render name section of link id 24299: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A tool for evaluate long-read de novo assembly results.<\/p>\n<!-- Time to render link large description section of link id 24299: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Inspector> How to use <\/a>\n<!-- Time to render notes section of link id 24299: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24299: 0.00030899047851562 --> \n<tr><td><a href=\"https:\/\/www.ebi.ac.uk\/interpro\/interproscan.html\" id=\"link-23649\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">InterProScan<\/a>\n<!-- Time to render name section of link id 23649: 5.0067901611328E-6 --> \n<\/td>\n<td><div>InterProScan is a tool that combines different protein signature recognition methods into one resource. No less than 14 pattern\/profiles databanks can be interrogated.<\/div>\n<!-- Time to render link large description section of link id 23649: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_InterProScan> How to use <\/a>\n<!-- Time to render notes section of link id 23649: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23649: 0.00029993057250977 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbbioconda\/wiki\/Improved-Phased-Assembler\" id=\"link-24323\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IPA<\/a>\n<!-- Time to render name section of link id 24323: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly.<\/p>\n<!-- Time to render link large description section of link id 24323: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IPA> How to use <\/a>\n<!-- Time to render notes section of link id 24323: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24323: 0.00029587745666504 --> \n<tr><td><a href=\"https:\/\/github.com\/phylo42\/IPK\" id=\"link-25430\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IPK<\/a>\n<!-- Time to render name section of link id 25430: 4.0531158447266E-6 --> \n<\/td>\n<td><p>IPK is a tool for computing phylo-k-mers for a fixed phylogeny.<\/p>\n<!-- Time to render link large description section of link id 25430: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IPK> How to use <\/a>\n<!-- Time to render notes section of link id 25430: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25430: 0.00029301643371582 --> \n<tr><td><a href=\"http:\/\/ipyrad.readthedocs.io\/\" id=\"link-23862\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ipyrad<\/a>\n<!-- Time to render name section of link id 23862: 4.0531158447266E-6 --> \n<\/td>\n<td><p>An interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.<\/p>\n<!-- Time to render link large description section of link id 23862: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ipyrad> How to use <\/a>\n<!-- Time to render notes section of link id 23862: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23862: 0.00030899047851562 --> \n<tr><td><a href=\"http:\/\/www.iqtree.org\/\" id=\"link-23860\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IQ-TREE<\/a>\n<!-- Time to render name section of link id 23860: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Efficient phylogenomic software by maximum likelihood<\/p>\n<!-- Time to render link large description section of link id 23860: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IQ-TREE> How to use <\/a>\n<!-- Time to render notes section of link id 23860: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23860: 0.00029921531677246 --> \n<tr><td><a href=\"https:\/\/github.com\/genemine\/iread\" id=\"link-24324\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iREAD<\/a>\n<!-- Time to render name section of link id 24324: 3.0994415283203E-6 --> \n<\/td>\n<td><p>iREAD (intron REtention Analysis and Detector)is a tool to detect intron retention(IR) events from RNA-seq datasets.<\/p>\n<!-- Time to render link large description section of link id 24324: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24324: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24324: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/RitchieLabIGH\/IRFinder\" id=\"link-24035\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IRFinder<\/a>\n<!-- Time to render name section of link id 24035: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Detecting intron retention from RNA-Seq experiments<\/p>\n<!-- Time to render link large description section of link id 24035: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IRFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24035: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24035: 0.00019717216491699 --> \n<tr><td><a href=\"https:\/\/github.com\/mkirsche\/Iris\" id=\"link-25321\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Iris<\/a>\n<!-- Time to render name section of link id 25321: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A module which corrects the sequences of structural variant calls (currently only insertions).<\/p>\n<!-- Time to render link large description section of link id 25321: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Iris> How to use <\/a>\n<!-- Time to render notes section of link id 25321: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25321: 0.00016593933105469 --> \n<tr><td><a href=\"https:\/\/wonder.cdc.gov\/amd\/flu\/irma\/\" id=\"link-24325\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IRMA<\/a>\n<!-- Time to render name section of link id 24325: 2.8610229492188E-6 --> \n<\/td>\n<td><p>IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza and ebolavirus. IRMA is free to use and parallelizes computations for both cluster computing and single computer multi-core setups.<\/p>\n<!-- Time to render link large description section of link id 24325: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IRMA> How to use <\/a>\n<!-- Time to render notes section of link id 24325: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24325: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/xiezhq\/ISEScan\" id=\"link-26177\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ISEScan<\/a>\n<!-- Time to render name section of link id 26177: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome.<\/p>\r\n<p>ISEScan can be used to identify\/annotate full-length or non-full-length IS elements in any DNA sequence but ISEScan was only tested on prokarytoic genome including draft genome and meta-genome.<\/p>\r\n<p>Among the existing tools identifying IS elements, ISEScan might be the only one that gives TIR (Terminal Inverted Repeat) sequences.<\/p>\n<!-- Time to render link large description section of link id 26177: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ISEScan> How to use <\/a>\n<!-- Time to render notes section of link id 26177: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26177: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/gvbarroso\/iSMC\" id=\"link-24326\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iSMC<\/a>\n<!-- Time to render name section of link id 24326: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This software extend the sequentially Markovian coalescent model to jointly infer the spatial variation in recombination rate (rho) from a single pair of unphased genomes.<\/p>\n<!-- Time to render link large description section of link id 24326: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24326: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24326: 0.00018191337585449 --> \n<tr><td><a href=\"http:\/\/alumni.cs.ucr.edu\/~liw\/isolasso.html\" id=\"link-24327\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IsoLasso<\/a>\n<!-- Time to render name section of link id 24327: 1.9073486328125E-6 --> \n<\/td>\n<td><p>IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.<\/p>\n<!-- Time to render link large description section of link id 24327: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24327: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24327: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/IsoSeq\" id=\"link-24328\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IsoSeq<\/a>\n<!-- Time to render name section of link id 24328: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads.<\/p>\n<!-- Time to render link large description section of link id 24328: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IsoSeq> How to use <\/a>\n<!-- Time to render notes section of link id 24328: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24328: 0.00020694732666016 --> \n<tr><td><a href=\"http:\/\/microbiology.se\/software\/itsx\/\" id=\"link-23650\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ITSx<\/a>\n<!-- Time to render name section of link id 23650: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing<\/p>\n<!-- Time to render link large description section of link id 23650: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ITSx> How to use <\/a>\n<!-- Time to render notes section of link id 23650: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23650: 0.00018119812011719 --> \n<tr><td><a href=\"https:\/\/github.com\/USDA-ARS-GBRU\/itsxpress\" id=\"link-25732\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ITSxpress<\/a>\n<!-- Time to render name section of link id 25732: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis.<\/p>\n<!-- Time to render link large description section of link id 25732: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ITSxpress> How to use <\/a>\n<!-- Time to render notes section of link id 25732: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25732: 0.00019097328186035 --> \n<tr><td><a href=\"http:\/\/sanger-pathogens.github.io\/iva\/\" id=\"link-23945\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IVA<\/a>\n<!-- Time to render name section of link id 23945: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Iterative Virus Assembler is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth<\/p>\n<!-- Time to render link large description section of link id 23945: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23945: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23945: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/andersen-lab\/ivar\" id=\"link-25121\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iVar<\/a>\n<!-- Time to render name section of link id 25121: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Var is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions\/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.<\/p>\n<!-- Time to render link large description section of link id 25121: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_iVar> How to use <\/a>\n<!-- Time to render notes section of link id 25121: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25121: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/biointec\/jabba\" id=\"link-24329\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jabba<\/a>\n<!-- Time to render name section of link id 24329: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A hybrid error correction tool for sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24329: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24329: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24329: 0.0001671314239502 --> \n<tr><td><a href=\"http:\/\/mcmc-jags.sourceforge.net\" id=\"link-24330\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JAGS<\/a>\n<!-- Time to render name section of link id 24330: 1.9073486328125E-6 --> \n<\/td>\n<td><p>JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.<\/p>\n<!-- Time to render link large description section of link id 24330: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JAGS> How to use <\/a>\n<!-- Time to render notes section of link id 24330: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24330: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/mkirsche\/Jasmine\" id=\"link-25042\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jasmine<\/a>\n<!-- Time to render name section of link id 25042: 2.8610229492188E-6 --> \n<\/td>\n<td><p dir=\"auto\">JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges. This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.<\/p>\r\n<p dir=\"auto\">Manual : <a href=\"https:\/\/github.com\/mkirsche\/Jasmine\/wiki\/Jasmine-User-Manual\">Jasmine User Manual \u00b7 mkirsche\/Jasmine Wiki \u00b7 GitHub<\/a><\/p>\r\n<p dir=\"auto\">Jasmine also includes a module for automating the creation of\u00a0<a href=\"http:\/\/software.broadinstitute.org\/software\/igv\/\" rel=\"nofollow\">IGV<\/a>\u00a0screenshots of variants of interest.<\/p>\n<!-- Time to render link large description section of link id 25042: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Jasmine> How to use <\/a>\n<!-- Time to render notes section of link id 25042: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25042: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/alguoo314\/jasper\" id=\"link-25059\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JASPER<\/a>\n<!-- Time to render name section of link id 25059: 1.9073486328125E-6 --> \n<\/td>\n<td><p dir=\"auto\">JASPER (Jellyfish based Assembly Sequence Polisher for Error Reduction) is an efficient polishing tool for draft genomes. It uses accurate reads (PacBio HiFi or Illumina) to evaluate consensus quality and correct consensus errors in genome assemblies. JASPER is substantially faster than polishing methods based on sequence alignment, and more accurate than currently available k-mer based methods. The efficiency and scalability of JASPER allows one to use it to create personalized reference genomes for specific populations very efficiently, even for large sequenced populations, by polishing the reference genome, such as GRCh38 or chm13v2.0 for human, with Illumina reads sequenced from many individuals from the population.<\/p>\r\n<p dir=\"auto\">Please see this manuscript for more details: Guo A, Salzberg SL, Zimin AV. JASPER: A fast genome polishing tool that improves accuracy of genome assemblies. PLoS Comput Biol. 2023 Mar 31;19(3):e1011032. doi: 10.1371\/journal.pcbi.1011032. PMID: 37000853; PMCID: PMC10096238.<\/p>\n<!-- Time to render link large description section of link id 25059: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JASPER> How to use <\/a>\n<!-- Time to render notes section of link id 25059: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25059: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/tanghaibao\/jcvi\" id=\"link-24332\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JCVI<\/a>\n<!-- Time to render name section of link id 24332: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.<\/p>\n<!-- Time to render link large description section of link id 24332: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JCVI> How to use <\/a>\n<!-- Time to render notes section of link id 24332: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24332: 0.00019407272338867 --> \n<tr><td><a href=\"http:\/\/www.cbcb.umd.edu\/software\/jellyfish\" id=\"link-23766\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jellyfish<\/a>\n<!-- Time to render name section of link id 23766: 3.0994415283203E-6 --> \n<\/td>\n<td><p>JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.<\/p>\n<!-- Time to render link large description section of link id 23766: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Jellyfish> How to use <\/a>\n<!-- Time to render notes section of link id 23766: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23766: 0.0001671314239502 --> \n<tr><td><a href=\"https:\/\/code.google.com\/p\/jmodeltest2\/\" id=\"link-23651\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">jModeltest<\/a>\n<!-- Time to render name section of link id 23651: 2.8610229492188E-6 --> \n<\/td>\n<td><p><strong>jModelTest<\/strong> is a tool to carry out statistical selection of best-fit models of nucleotide substitution.<\/p>\n<!-- Time to render link large description section of link id 23651: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23651: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23651: 0.0001978874206543 --> \n<tr><td><a href=\"http:\/\/jphmm.gobics.de\/jphmm.html\" id=\"link-25985\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">jpHMM<\/a>\n<!-- Time to render name section of link id 25985: 3.0994415283203E-6 --> \n<\/td>\n<td><p>jpHMM (jumping profile Hidden Markov Model) is a probabilistic approach to compare a sequence to a multiple alignment of a sequence family. The jpHMM web server at GOBICS is a tool for the detection of recombinations in\u00a0<a href=\"http:\/\/jphmm.gobics.de\/submission_hiv\">HIV-1<\/a>\u00a0and\u00a0<a href=\"http:\/\/jphmm.gobics.de\/submission_hbv\">hepatitis B virus (HBV)<\/a> genomes.<br \/>\r\nFor a query sequence phylogenetic recombination breakpoints are predicted and each region of the sequence is assigned to one HIV-1 subtype\/HBV genotype. This prediction is based on a pre-calculated multiple alignment of the major HIV-1 subtypes\/HBV genotypes. A detailed description of the algorithm and some information about the evaluation can be found\u00a0<a href=\"http:\/\/jphmm.gobics.de\/method.html\">here<\/a>. For information about the output format please see the\u00a0<a href=\"http:\/\/jphmm.gobics.de\/submission\">online submission<\/a>\u00a0page.<\/p>\n<!-- Time to render link large description section of link id 25985: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_jpHMM> How to use <\/a>\n<!-- Time to render notes section of link id 25985: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25985: 0.00022697448730469 --> \n<tr><td><a href=\"http:\/\/aidenlab.org\/juicebox\/\" id=\"link-23797\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Juicebox<\/a>\n<!-- Time to render name section of link id 23797: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software for visualizing data from Hi-C and other proximity mapping experiments<\/p>\n<!-- Time to render link large description section of link id 23797: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23797: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23797: 0.00016593933105469 --> \n<tr><td><a href=\"https:\/\/github.com\/phasegenomics\/juicebox_scripts\" id=\"link-24333\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">juicebox_scripts<\/a>\n<!-- Time to render name section of link id 24333: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats<\/p>\n<!-- Time to render link large description section of link id 24333: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24333: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24333: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/theaidenlab\/juicer\/\" id=\"link-23784\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Juicer<\/a>\n<!-- Time to render name section of link id 23784: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A One-Click System for Analyzing Loop-Resolution Hi-C Experiments<\/p>\n<!-- Time to render link large description section of link id 23784: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Juicer> How to use <\/a>\n<!-- Time to render notes section of link id 23784: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23784: 0.00016689300537109 --> \n<tr><td><a href=\"http:\/\/julialang.org\/\" id=\"link-23833\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Julia<\/a>\n<!-- Time to render name section of link id 23833: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library.<\/p>\n<!-- Time to render link large description section of link id 23833: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Julia> How to use <\/a>\n<!-- Time to render notes section of link id 23833: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23833: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/ridgelab\/JustOrthologs\" id=\"link-23976\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JustOrthologs<\/a>\n<!-- Time to render name section of link id 23976: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Fast, Accurate, and User-Friendly Ortholog-Finding Algorithm<\/p>\n<!-- Time to render link large description section of link id 23976: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23976: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23976: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/lindenb\/jvarkit\" id=\"link-24334\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jvarkit<\/a>\n<!-- Time to render name section of link id 24334: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Java utilities for Bioinformatics (only requested tools are compiling)<\/p>\n<!-- Time to render link large description section of link id 24334: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24334: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24334: 0.0001678466796875 --> \n<tr><td><a href=\"https:\/\/github.com\/liu3zhenlab\/kad\" id=\"link-24335\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KAD<\/a>\n<!-- Time to render name section of link id 24335: 3.0994415283203E-6 --> \n<\/td>\n<td><p>KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24335: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24335: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24335: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinformatics-centre\/kaiju\" id=\"link-23804\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Kaiju<\/a>\n<!-- Time to render name section of link id 23804: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Fast taxonomic classification of metagenomic sequencing reads using a protein reference database<\/p>\n<!-- Time to render link large description section of link id 23804: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Kaiju> How to use <\/a>\n<!-- Time to render notes section of link id 23804: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23804: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/pachterlab.github.io\/kallisto\/\" id=\"link-23816\" class=\"track_this_link \" rel=\"noopener noreferrer\">kallisto<\/a>\n<!-- Time to render name section of link id 23816: 1.9073486328125E-6 --> \n<\/td>\n<td><p>kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 23816: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kallisto> How to use <\/a>\n<!-- Time to render notes section of link id 23816: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23816: 0.00018191337585449 --> \n<tr><td><a href=\"http:\/\/www.earlham.ac.uk\/kat-tools\" id=\"link-23955\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KAT<\/a>\n<!-- Time to render name section of link id 23955: 2.1457672119141E-6 --> \n<\/td>\n<td><p>KAT (The K-mer Analysis Toolkit) is a suite of tools that generate, analyse and compare k-mer spectra produced from sequence files.<\/p>\n<!-- Time to render link large description section of link id 23955: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KAT> How to use <\/a>\n<!-- Time to render notes section of link id 23955: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23955: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/kcoss-2021\/KCOSS\" id=\"link-24742\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KCOSS<\/a>\n<!-- Time to render name section of link id 24742: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and space-saving multi-threaded k-mer frequency statistics algorithm<\/p>\n<!-- Time to render link large description section of link id 24742: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24742: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24742: 0.0001680850982666 --> \n<tr><td><a href=\"https:\/\/github.com\/ENCODE-DCC\/kentUtils\" id=\"link-23826\" class=\"track_this_link \" rel=\"noopener noreferrer\">kentUtils<\/a>\n<!-- Time to render name section of link id 23826: 2.1457672119141E-6 --> \n<\/td>\n<td><p>UCSC command line bioinformatic utilities<\/p>\n<!-- Time to render link large description section of link id 23826: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kentUtils> How to use <\/a>\n<!-- Time to render notes section of link id 23826: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23826: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/dib-lab\/khmer\" id=\"link-26171\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">khmer<\/a>\n<!-- Time to render name section of link id 26171: 2.1457672119141E-6 --> \n<\/td>\n<td><p>In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more.<\/p>\r\n<p><a href=\"https:\/\/khmer.readthedocs.io\/en\/latest\/\">The khmer software for advanced biological sequencing data analysis \u2014 khmer 3.0.0a1+98.gfe0ce11 documentation<\/a><\/p>\n<!-- Time to render link large description section of link id 26171: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_khmer> How to use <\/a>\n<!-- Time to render notes section of link id 26171: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26171: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/ldenti\/klocate\" id=\"link-24337\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">klocate<\/a>\n<!-- Time to render name section of link id 24337: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Standalone tool based on the bwa index to locate a set of kmers along a reference genome. klocate searches each kmer (full and perfect match) in the index and outputs all positions the kmer maps to (output to sdtout in bed format).<\/p>\n<!-- Time to render link large description section of link id 24337: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24337: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24337: 0.0001671314239502 --> \n<tr><td><a href=\"https:\/\/catchenlab.life.illinois.edu\/klumpy\/\" id=\"link-26205\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">klumpy<\/a>\n<!-- Time to render name section of link id 26205: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Klumpy is a bioinformatic tool for identifying possibly incorrectly assembled regions in a long-read based assembly, with the additional capabilities of annotating sequences given a set of query sequences.<\/p>\n<!-- Time to render link large description section of link id 26205: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_klumpy> How to use <\/a>\n<!-- Time to render notes section of link id 26205: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26205: 0.00021004676818848 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/kma\" id=\"link-24114\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KMA<\/a>\n<!-- Time to render name section of link id 24114: 2.8610229492188E-6 --> \n<\/td>\n<td><p>KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.<\/p>\n<!-- Time to render link large description section of link id 24114: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KMA> How to use <\/a>\n<!-- Time to render notes section of link id 24114: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24114: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/ldenti\/kmap\" id=\"link-24338\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmap<\/a>\n<!-- Time to render name section of link id 24338: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Standalone tool based on the bwa index to locate a set of kmers along a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24338: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24338: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24338: 0.00018095970153809 --> \n<tr><td><a href=\"http:\/\/sun.aei.polsl.pl\/REFRESH\/index.php?page=projects&#038;#038\" id=\"link-24339\" class=\"track_this_link \" rel=\"noopener noreferrer\">KMC<\/a>\n<!-- Time to render name section of link id 24339: 1.9073486328125E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 24339: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KMC> How to use <\/a>\n<!-- Time to render notes section of link id 24339: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24339: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/tlemane\/kmdiff\" id=\"link-24749\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmdiif<\/a>\n<!-- Time to render name section of link id 24749: 1.9073486328125E-6 --> \n<\/td>\n<td><p>kmdiff provides differential k-mers analysis between two populations (control and case). Each population is represented by a set of short-read sequencing. Outputs are differentially represented k-mers between controls and cases.<\/p>\n<!-- Time to render link large description section of link id 24749: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kmdiff> How to use <\/a>\n<!-- Time to render notes section of link id 24749: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24749: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/kmer-counter\" id=\"link-25440\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmer-counter<\/a>\n<!-- Time to render name section of link id 25440: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A fast k-mer counter written in Rust.<\/p>\n<!-- Time to render link large description section of link id 25440: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kmer-counter> How to use <\/a>\n<!-- Time to render notes section of link id 25440: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25440: 0.00018095970153809 --> \n<tr><td><a href=\"http:\/\/kmergenie.bx.psu.edu\/\" id=\"link-23652\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KmerGenie<\/a>\n<!-- Time to render name section of link id 23652: 2.8610229492188E-6 --> \n<\/td>\n<td><p>KmerGenie estimates the best k-mer length for genome de novo assembly.<\/p>\n<!-- Time to render link large description section of link id 23652: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KmerGenie> How to use <\/a>\n<!-- Time to render notes section of link id 23652: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23652: 0.00018215179443359 --> \n<tr><td><a href=\"https:\/\/github.com\/ChnMasterOG\/KmerGO\" id=\"link-26026\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KmerGO<\/a>\n<!-- Time to render name section of link id 26026: 2.1457672119141E-6 --> \n<\/td>\n<td><p>KmerGO is a user-friendly tool to identify the group-specific sequences on two groups or trait-associated sequences of high throughput sequencing datasets.<\/p>\n<!-- Time to render link large description section of link id 26026: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KmerGO> How to use <\/a>\n<!-- Time to render notes section of link id 26026: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26026: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/voichek\/kmersGWAS\" id=\"link-25316\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmersGWAS<\/a>\n<!-- Time to render name section of link id 25316: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A library for running k-mers based GWAS.<\/p>\n<!-- Time to render link large description section of link id 25316: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kmersGWAS> How to use <\/a>\n<!-- Time to render notes section of link id 25316: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25316: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/takaram\/kofam_scan\" id=\"link-24839\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KofamScan<\/a>\n<!-- Time to render name section of link id 24839: 3.0994415283203E-6 --> \n<\/td>\n<td><p>KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model<\/p>\n<!-- Time to render link large description section of link id 24839: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KofamScan> How to use <\/a>\n<!-- Time to render notes section of link id 24839: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24839: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/eclarke\/komplexity\" id=\"link-24340\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">komplexity<\/a>\n<!-- Time to render name section of link id 24340: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A command-line tool built in Rust to quickly calculate and\/or mask low-complexity sequences from a FAST<A\/Q> file. This uses the number of unique k-mers over a sequence divided by the length to assess complexity.<\/p>\n<!-- Time to render link large description section of link id 24340: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_komplexity> How to use <\/a>\n<!-- Time to render notes section of link id 24340: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24340: 0.00018215179443359 --> \n<tr><td><a href=\"http:\/\/ccb.jhu.edu\/software\/kraken\/\" id=\"link-23908\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Kraken<\/a>\n<!-- Time to render name section of link id 23908: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.<\/p>\n<!-- Time to render link large description section of link id 23908: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23908: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23908: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/DerrickWood\/kraken2\" id=\"link-24053\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Kraken2<\/a>\n<!-- Time to render name section of link id 24053: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.<\/p>\n<!-- Time to render link large description section of link id 24053: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Kraken2> How to use <\/a>\n<!-- Time to render notes section of link id 24053: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24053: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/github.com\/jenniferlu717\/KrakenTools\" id=\"link-25601\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KrakenTools<\/a>\n<!-- Time to render name section of link id 25601: 3.0994415283203E-6 --> \n<\/td>\n<td><p>KrakenTools provides individual scripts to analyze Kraken\/Kraken2\/Bracken\/KrakenUniq output files.<\/p>\n<!-- Time to render link large description section of link id 25601: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KrakenTools> How to use <\/a>\n<!-- Time to render notes section of link id 25601: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25601: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/fbreitwieser\/krakenuniq\" id=\"link-24119\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KrakenUniq<\/a>\n<!-- Time to render name section of link id 24119: 1.9073486328125E-6 --> \n<\/td>\n<td><p>KrakenUniq (formerly KrakenHLL) is a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset.<\/p>\n<!-- Time to render link large description section of link id 24119: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KrakenUniq> How to use <\/a>\n<!-- Time to render notes section of link id 24119: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24119: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/Krona\/wiki\" id=\"link-23653\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Krona<\/a>\n<!-- Time to render name section of link id 23653: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Krona allows hierarchical data to be explored with zoomable pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats.<\/p>\n<!-- Time to render link large description section of link id 23653: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Krona> How to use <\/a>\n<!-- Time to render notes section of link id 23653: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23653: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/ksnp\/\" id=\"link-25283\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kSNP4<\/a>\n<!-- Time to render name section of link id 25283: 3.0994415283203E-6 --> \n<\/td>\n<td><p>kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.<\/p>\n<!-- Time to render link large description section of link id 25283: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kSNP4> How to use <\/a>\n<!-- Time to render notes section of link id 25283: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25283: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/shendurelab\/LACHESIS\" id=\"link-23932\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LACHESIS<\/a>\n<!-- Time to render name section of link id 23932: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software that uses Hi-C data for ultra-long-range scaffolding of de novo genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 23932: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23932: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23932: 0.00031518936157227 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/mcfrith\/lamassemble\" id=\"link-24341\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lamassemble<\/a>\n<!-- Time to render name section of link id 24341: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Merge overlapping \"long\" DNA reads into a consensus sequence.<\/p>\n<!-- Time to render link large description section of link id 24341: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24341: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24341: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/mcfrith\/last\" id=\"link-23654\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LAST<\/a>\n<!-- Time to render name section of link id 23654: 3.0994415283203E-6 --> \n<\/td>\n<td><p>LAST finds similar regions between sequences.<\/p>\n<!-- Time to render link large description section of link id 23654: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LAST> How to use <\/a>\n<!-- Time to render notes section of link id 23654: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23654: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/faylward\/lastp_aai\" id=\"link-24342\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lastp_aai<\/a>\n<!-- Time to render name section of link id 24342: 7.8678131103516E-6 --> \n<\/td>\n<td><p>A simple Python script for calculating pairwise amino acid identity (AAI) between protein files (extension .faa)<\/p>\n<!-- Time to render link large description section of link id 24342: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24342: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24342: 0.00055789947509766 --> \n<tr><td><a href=\"http:\/\/www.bx.psu.edu\/miller_lab\/dist\/README.lastz-1.02.00\/README.lastz-1.02.00a.html#install\" id=\"link-23852\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LASTZ<\/a>\n<!-- Time to render name section of link id 23852: 8.1062316894531E-6 --> \n<\/td>\n<td><p>A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically.<\/p>\n<!-- Time to render link large description section of link id 23852: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LASTZ> How to use <\/a>\n<!-- Time to render notes section of link id 23852: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23852: 0.00061511993408203 --> \n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/maximum-likelihood-relatedness-estimation\" id=\"link-24343\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lcMLkin<\/a>\n<!-- Time to render name section of link id 24343: 6.9141387939453E-6 --> \n<\/td>\n<td><p>lcMLkin is a C++ program that allows users to infer biological relatedness from low coverage 2nd generation sequencing data<\/p>\n<!-- Time to render link large description section of link id 24343: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24343: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24343: 0.00051999092102051 --> \n<tr><td><a href=\"http:\/\/ldhat.sourceforge.net\/instructions.shtml\" id=\"link-23655\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LDhat<\/a>\n<!-- Time to render name section of link id 23655: 6.9141387939453E-6 --> \n<\/td>\n<td><p>LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.<\/p>\n<!-- Time to render link large description section of link id 23655: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23655: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23655: 0.00052189826965332 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenmethods\/LDhelmet\" id=\"link-23656\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LDhelmet<\/a>\n<!-- Time to render name section of link id 23656: 8.1062316894531E-6 --> \n<\/td>\n<td><p>LDhelmet performs statistical inference for fine-scale variable recombination rate estimation.<\/p>\n<!-- Time to render link large description section of link id 23656: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LDhelmet> How to use <\/a>\n<!-- Time to render notes section of link id 23656: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23656: 0.00049996376037598 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/leeHom\" id=\"link-24344\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">leeHom<\/a>\n<!-- Time to render name section of link id 24344: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A program for the Bayesian reconstruction of ancient DNA.<\/p>\n<!-- Time to render link large description section of link id 24344: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24344: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24344: 0.00049614906311035 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/nsegata\/lefse\" id=\"link-23940\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LEfSe<\/a>\n<!-- Time to render name section of link id 23940: 8.1062316894531E-6 --> \n<\/td>\n<td><p>LEfSe (Linear discriminant analysis effect size) is a tool developed by the Huttenhower group to find biomarkers between 2 or more groups using relative abundances.<\/p>\n<!-- Time to render link large description section of link id 23940: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LEfSe> How to use <\/a>\n<!-- Time to render notes section of link id 23940: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23940: 0.00049781799316406 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/lep-map3\" id=\"link-24729\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Lep-MAP3<\/a>\n<!-- Time to render name section of link id 24729: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Lep-MAP3 is a novel and free software for linkage mapping. It can construct linkage maps on very large number of markers and individuals on single or multiple families.<\/p>\n<!-- Time to render link large description section of link id 24729: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Lep-MAP3> How to use <\/a>\n<!-- Time to render notes section of link id 24729: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24729: 0.00025200843811035 --> \n<tr><td><a href=\"https:\/\/github.com\/mfranberg\/libplinkio\" id=\"link-24023\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">libplinkio<\/a>\n<!-- Time to render name section of link id 24023: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This is a small C and Python library for reading Plink genotype files.<\/p>\n<!-- Time to render link large description section of link id 24023: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_libplinkio> How to use <\/a>\n<!-- Time to render notes section of link id 24023: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24023: 0.00024700164794922 --> \n<tr><td><a href=\"http:\/\/www.icir.org\/christian\/libstree\/\" id=\"link-24345\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">libstree<\/a>\n<!-- Time to render name section of link id 24345: 4.0531158447266E-6 --> \n<\/td>\n<td><p>libstree is a generic suffix tree implementation, written in C.<\/p>\n<!-- Time to render link large description section of link id 24345: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_libstree> How to use <\/a>\n<!-- Time to render notes section of link id 24345: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24345: 0.00023388862609863 --> \n<tr><td><a href=\"https:\/\/github.com\/agshumate\/Liftoff\" id=\"link-24346\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Liftoff<\/a>\n<!-- Time to render name section of link id 24346: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.<\/p>\n<!-- Time to render link large description section of link id 24346: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Liftoff> How to use <\/a>\n<!-- Time to render notes section of link id 24346: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24346: 0.00024294853210449 --> \n<tr><td><a href=\"https:\/\/github.com\/pacificbiosciences\/barcoding\/\" id=\"link-24347\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lima<\/a>\n<!-- Time to render name section of link id 24347: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Demultiplex Barcoded PacBio Samples.<\/p>\n<!-- Time to render link large description section of link id 24347: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24347: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24347: 0.00024890899658203 --> \n<tr><td><a href=\"https:\/\/github.com\/rwtourdot\/linker\" id=\"link-24348\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Linker<\/a>\n<!-- Time to render name section of link id 24348: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Linker is a suite of C++ tools useful for interpreting long and linked read sequencing of cancer genomes.<\/p>\n<!-- Time to render link large description section of link id 24348: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24348: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24348: 0.00023603439331055 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/LINKS\" id=\"link-23936\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LINKS<\/a>\n<!-- Time to render name section of link id 23936: 3.0994415283203E-6 --> \n<\/td>\n<td><p>LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences.<\/p>\n<!-- Time to render link large description section of link id 23936: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LINKS> How to use <\/a>\n<!-- Time to render notes section of link id 23936: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23936: 0.00023794174194336 --> \n<tr><td><a href=\"https:\/\/github.com\/WGLab\/LIQA\" id=\"link-24349\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LIQA<\/a>\n<!-- Time to render name section of link id 24349: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Long-read Isoform Quantification and Analysis) is an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data.<\/p>\n<!-- Time to render link large description section of link id 24349: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24349: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24349: 0.0002598762512207 --> \n<tr><td><a href=\"https:\/\/github.com\/AntonBankevich\/LJA\" id=\"link-24350\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LJA<\/a>\n<!-- Time to render name section of link id 24350: 4.0531158447266E-6 --> \n<\/td>\n<td><p>La Jolla Assembler (LJA) is a tool for genome assembly from HiFI reads based on de Bruijn graphs.<\/p>\n<!-- Time to render link large description section of link id 24350: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LJA> How to use <\/a>\n<!-- Time to render notes section of link id 24350: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24350: 0.00024890899658203 --> \n<tr><td><a href=\"https:\/\/llvm.org\/\" id=\"link-23897\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">llvm<\/a>\n<!-- Time to render name section of link id 23897: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.<\/p>\n<!-- Time to render link large description section of link id 23897: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23897: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23897: 0.00023913383483887 --> \n<tr><td><a href=\"https:\/\/github.com\/JanaSperschneider\/LOCALIZER\" id=\"link-25471\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LOCALIZER<\/a>\n<!-- Time to render name section of link id 25471: 2.8610229492188E-6 --> \n<\/td>\n<td><p>LOCALIZER is a machine learning method for predicting the subcellular localization of both plant proteins and pathogen effectors in the plant cell.<\/p>\n<!-- Time to render link large description section of link id 25471: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LOCALIZER> How to use <\/a>\n<!-- Time to render notes section of link id 25471: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25471: 0.00023794174194336 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-freiburg.de\/Software\/LocARNA\/\" id=\"link-24351\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LocARNA<\/a>\n<!-- Time to render name section of link id 24351: 4.0531158447266E-6 --> \n<\/td>\n<td><p>LocARNA is a tool for multiple alignment of RNA molecules. LocARNA requires only RNA sequences as input and will simultaneously fold and align the input sequences.<\/p>\n<!-- Time to render link large description section of link id 24351: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24351: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24351: 0.00023508071899414 --> \n<tr><td><a href=\"https:\/\/github.com\/kr-colab\/locator\" id=\"link-24352\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">locator<\/a>\n<!-- Time to render name section of link id 24352: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A supervised machine learning method for predicting the geographic origin of a sample from genotype or sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24352: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_locator> How to use <\/a>\n<!-- Time to render notes section of link id 24352: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24352: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/sudmantlab\/loco-pipe\" id=\"link-25804\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">loco-pipe<\/a>\n<!-- Time to render name section of link id 25804: 3.0994415283203E-6 --> \n<\/td>\n<td><p>loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data.<\/p>\n<!-- Time to render link large description section of link id 25804: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_loco-pipe> How to use <\/a>\n<!-- Time to render notes section of link id 25804: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25804: 0.00018215179443359 --> \n<tr><td><a href=\"https:\/\/github.com\/Rostlab\/LocTree3\" id=\"link-23796\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Loctree3<\/a>\n<!-- Time to render name section of link id 23796: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Protein Subcelullar Localization Sequenced-Based Predictor<\/p>\n<!-- Time to render link large description section of link id 23796: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LocTree> How to use <\/a>\n<!-- Time to render notes section of link id 23796: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23796: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/CSB5\/lofreq\" id=\"link-24353\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LoFreq<\/a>\n<!-- Time to render name section of link id 24353: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A sequence-quality aware, ultra-sensitive variant caller for NGS data.<\/p>\n<!-- Time to render link large description section of link id 24353: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LoFreq> How to use <\/a>\n<!-- Time to render notes section of link id 24353: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24353: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/longdust\" id=\"link-26089\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">longdust<\/a>\n<!-- Time to render name section of link id 26089: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Longdust identifies long highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs) in a genome.<\/p>\n<!-- Time to render link large description section of link id 26089: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_longdust> How to use <\/a>\n<!-- Time to render notes section of link id 26089: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26089: 0.00020599365234375 --> \n<tr><td><a href=\"https:\/\/github.com\/yfukasawa\/LongQC\" id=\"link-24354\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LongQC<\/a>\n<!-- Time to render name section of link id 24354: 1.9073486328125E-6 --> \n<\/td>\n<td><p>LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc.<\/p>\n<!-- Time to render link large description section of link id 24354: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LongQC> How to use <\/a>\n<!-- Time to render notes section of link id 24354: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24354: 0.00020289421081543 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/genome-exome\/software\/pipelines\/latest\/what-is-long-ranger\" id=\"link-23879\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LongRanger<\/a>\n<!-- Time to render name section of link id 23879: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.<\/p>\n<!-- Time to render link large description section of link id 23879: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LongRanger> How to use <\/a>\n<!-- Time to render notes section of link id 23879: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23879: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/pjedge\/longshot\" id=\"link-24355\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">longshot<\/a>\n<!-- Time to render name section of link id 24355: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).<\/p>\n<!-- Time to render link large description section of link id 24355: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24355: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24355: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/longstitch\" id=\"link-24356\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LongStitch<\/a>\n<!-- Time to render name section of link id 24356: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A genome assembly correction and scaffolding pipeline using long reads. Basically runs Tigmint, ntLink, ARKS.<\/p>\n<!-- Time to render link large description section of link id 24356: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24356: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24356: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/github.com\/BioinformaticsToolsmith\/Look4TRs\" id=\"link-25164\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Look4TRs<\/a>\n<!-- Time to render name section of link id 25164: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A de-novo tool for detecting simple tandem repeats using self-supervised hidden Markov models.<\/p>\n<!-- Time to render link large description section of link id 25164: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Look4TRs> How to use <\/a>\n<!-- Time to render notes section of link id 25164: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25164: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/atgc.lirmm.fr\/lordec\/\" id=\"link-23657\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LoRDEC<\/a>\n<!-- Time to render name section of link id 23657: 2.1457672119141E-6 --> \n<\/td>\n<td><p>LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.<\/p>\n<!-- Time to render link large description section of link id 23657: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LoRDEC> How to use <\/a>\n<!-- Time to render notes section of link id 23657: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23657: 0.00017619132995605 --> \n<tr><td><a href=\"http:\/\/www.fishbrowser.org\/software\/LR_Gapcloser\/index.php\/Home\/Index\/Index.html\" id=\"link-24030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LR_Gapcloser<\/a>\n<!-- Time to render name section of link id 24030: 1.9073486328125E-6 --> \n<\/td>\n<td><p>\u00a0LR_Gapcloser is a gap closing tool using uncorrected or corrected long reads generated from Pacbio platform or Nanopore platform.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24030: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24030: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24030: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/LRez\" id=\"link-24357\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRez<\/a>\n<!-- Time to render name section of link id 24357: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Standalone tool and library allowing to work with barcoded linked-reads.<\/p>\n<!-- Time to render link large description section of link id 24357: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24357: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24357: 0.00019311904907227 --> \n<tr><td><a href=\"https:\/\/github.com\/shingocat\/lrscaf\" id=\"link-23977\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRScaf<\/a>\n<!-- Time to render name section of link id 23977: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TGS scaffolding . Improving draft genomes using long noisy reads.<\/p>\n<!-- Time to render link large description section of link id 23977: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23977: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23977: 0.00016117095947266 --> \n<tr><td><a href=\"https:\/\/github.com\/aquaskyline\/LRSIM\" id=\"link-24358\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRSIM<\/a>\n<!-- Time to render name section of link id 24358: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Simulator for Linked Reads: this package simulates whole genome sequencing using 10X Genomics Linked Read technology.<\/p>\n<!-- Time to render link large description section of link id 24358: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24358: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24358: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/carlosj-rr\/LSx\" id=\"link-25040\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LSx<\/a>\n<!-- Time to render name section of link id 25040: 1.9073486328125E-6 --> \n<\/td>\n<td><p>LS<sup>X<\/sup>\u00a0is a script in R that runs the LS\u00b3 and LS\u2074 algorithms of data subsampling for multigene phylogenetic inference. Both of these algorithms do a gene-by-gene inspection of the heterogeneity of evolutionary rates among user-defined lineages of interest (LOI). Then, using criteria that differ in both algorithms (see details\u00a0<a href=\"https:\/\/github.com\/carlosj-rr\/LSx\/wiki\/Introduction#is-lsx-for-me\">here<\/a>\u00a0or in the\u00a0<a href=\"https:\/\/github.com\/carlosj-rr\/LSx\/wiki\/Citations\">papers<\/a>), they try to find a subsample of sequences that evolve at a homogeneous rate across all LOIs. If this subset is found, an alignment of the gene is produced with only the sequences that evolve homogeneously. At the same time, a table is also produced showing which sequences were \u201cflagged\u201d (the sequences that were removed), and which sequences were kept. If a subset of sequences that evolve at a homogeneous rate is not found, the gene is flagged entirely.<\/p>\n<!-- Time to render link large description section of link id 25040: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LSx> How to use <\/a>\n<!-- Time to render notes section of link id 25040: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25040: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/TulsaBioinformaticsToolsmith\/LtrDetector\" id=\"link-24360\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LtrDetector<\/a>\n<!-- Time to render name section of link id 24360: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool-suite for detecting long terminal repeat retrotransposons de-novo on the genomic scale.<\/p>\n<!-- Time to render link large description section of link id 24360: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LtrDetector> How to use <\/a>\n<!-- Time to render notes section of link id 24360: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24360: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/arq5x\/lumpy-sv\" id=\"link-23918\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LUMPY<\/a>\n<!-- Time to render name section of link id 23918: 0.0001528263092041 --> \n<\/td>\n<td><p>A general probabilistic framework for structural variant discovery<\/p>\n<!-- Time to render link large description section of link id 23918: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LUMPY> How to use <\/a>\n<!-- Time to render notes section of link id 23918: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23918: 0.00032997131347656 --> \n<tr><td><a href=\"http:\/\/csg.sph.umich.edu\/abecasis\/MaCH\/\" id=\"link-23961\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MACH<\/a>\n<!-- Time to render name section of link id 23961: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MACH is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.<\/p>\n<!-- Time to render link large description section of link id 23961: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23961: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23961: 0.0001981258392334 --> \n<tr><td><a href=\"https:\/\/github.com\/macs3-project\/MACS\" id=\"link-23659\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MACS<\/a>\n<!-- Time to render name section of link id 23659: 3.0994415283203E-6 --> \n<\/td>\n<td><p>We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina \/ Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples.<\/p>\n<!-- Time to render link large description section of link id 23659: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MACS> How to use <\/a>\n<!-- Time to render notes section of link id 23659: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23659: 0.00020003318786621 --> \n<tr><td><a href=\"https:\/\/bioweb.supagro.inra.fr\/macse\/\" id=\"link-24361\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MACSE<\/a>\n<!-- Time to render name section of link id 24361: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons: a wide range of molecular analyses relies on multiple sequence alignments (MSA).<\/p>\n<!-- Time to render link large description section of link id 24361: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24361: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24361: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/gem-pasteur\/macsyfinder\/\" id=\"link-26122\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MacSyFinder<\/a>\n<!-- Time to render name section of link id 26122: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Detection of macromolecular systems in protein datasets using systems modelling and similarity search.<\/p>\r\n<p>Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system.\u00a0<\/p>\n<!-- Time to render link large description section of link id 26122: 0.0005948543548584 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MacSyFinder> How to use <\/a>\n<!-- Time to render notes section of link id 26122: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26122: 0.00078988075256348 --> \n<tr><td><a href=\"https:\/\/pbwww.services.came.sbg.ac.at\/?page_id=416\" id=\"link-25154\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAESTRO<\/a>\n<!-- Time to render name section of link id 25154: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Multi AgEnt STability pRedictiOn tool for changes in unfolding free energy upon point mutation.<\/p>\r\n<p>MAESTRO is structure based and distinguishes from similar approaches in the following points: (i) MAESTRO implements a multi-agent machine learning system. (ii) It provides predicted \u0394\u0394G values along with a corresponding prediction quality measure. (iii) MAESTRO is applicable to biological assemblies. (iv) It provides high throughput scanning for multi-point mutations where sites and types of mutation can be comprehensively controlled. (v) Finally, the software provides a specific mode for the prediction of stabilizing disulfide bonds.<\/p>\n<!-- Time to render link large description section of link id 25154: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAESTRO> How to use <\/a>\n<!-- Time to render notes section of link id 25154: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25154: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/mafft.cbrc.jp\/alignment\/software\/\" id=\"link-23658\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAFFT<\/a>\n<!-- Time to render name section of link id 23658: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MAFFT is a multiple sequence alignment program for unix-like operating systems.\u00a0 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of &lt;?200 sequences), FFT-NS-2 (fast; for alignment of &lt;?10,000 sequences), <i>etc<\/i>.<\/p>\n<!-- Time to render link large description section of link id 23658: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAFFT> How to use <\/a>\n<!-- Time to render notes section of link id 23658: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23658: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/liulab-dfci\/MAGeCK\" id=\"link-25102\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAGeCK<\/a>\n<!-- Time to render name section of link id 25102: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.<br \/>\r\nMAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR\/Cas9 screens.<br \/>\r\nMAGeCKFlute (R package):Integrative analysis pipeline for pooled CRISPR functional genetic screens<\/p>\r\n<p>Manual and video tutorials : <a href=\"https:\/\/bitbucket.org\/liulab\/mageck-vispr\/src\/master\/\">liulab \/ mageck-vispr \u2014 Bitbucket<\/a><\/p>\n<!-- Time to render link large description section of link id 25102: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAGeCK> How to use <\/a>\n<!-- Time to render notes section of link id 25102: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25102: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/asroopra\/MAGIC\" id=\"link-24362\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAGIC<\/a>\n<!-- Time to render name section of link id 24362: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data.<\/p>\n<!-- Time to render link large description section of link id 24362: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24362: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24362: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/ncbi.github.io\/magicblast\/\" id=\"link-24363\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Magic-BLAST<\/a>\n<!-- Time to render name section of link id 24363: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.<\/p>\n<!-- Time to render link large description section of link id 24363: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Magic-BLAST> How to use <\/a>\n<!-- Time to render notes section of link id 24363: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24363: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/www.yandell-lab.org\/software\/maker.html\" id=\"link-24064\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAKER<\/a>\n<!-- Time to render name section of link id 24064: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.<\/p>\n<!-- Time to render link large description section of link id 24064: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAKER> How to use <\/a>\n<!-- Time to render notes section of link id 24064: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24064: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/joepickrell\/malder\" id=\"link-23786\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MALDER<\/a>\n<!-- Time to render name section of link id 23786: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This is a version of ALDER (http:\/\/groups.csail.mit.edu\/cb\/alder\/) that has been modified to allow multiple admixture events.<\/p>\n<!-- Time to render link large description section of link id 23786: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MALDER> How to use <\/a>\n<!-- Time to render notes section of link id 23786: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23786: 0.00018405914306641 --> \n<tr><td><a href=\"http:\/\/ab.inf.uni-tuebingen.de\/software\/malt\/\" id=\"link-24057\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MALT<\/a>\n<!-- Time to render name section of link id 24057: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MALT (MEGAN alignment tool) is an extension of MEGAN (metagenome analyzer).<br \/>\r\nMALT performs alignment of metagenomic reads against a database of reference sequences (such as NR, GenBank or Silva) and produces a MEGAN RMA file as output. The software is currently under development.<\/p>\n<!-- Time to render link large description section of link id 24057: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MALT> How to use <\/a>\n<!-- Time to render notes section of link id 24057: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24057: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/manta\" id=\"link-24364\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Manta<\/a>\n<!-- Time to render name section of link id 24364: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24364: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Manta> How to use <\/a>\n<!-- Time to render notes section of link id 24364: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24364: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/ginolhac.github.io\/mapDamage\/\" id=\"link-23909\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mapDamage<\/a>\n<!-- Time to render name section of link id 23909: 1.9073486328125E-6 --> \n<\/td>\n<td><p>tracking and quantifying damage patterns in ancient DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 23909: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mapDamage> How to use <\/a>\n<!-- Time to render notes section of link id 23909: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23909: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/colibread.inria.fr\/software\/mapsembler2\/\" id=\"link-23935\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mapsembler2<\/a>\n<!-- Time to render name section of link id 23935: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Mapsembler2 is a targeted assembly software. It takes as input any number of NGS raw read set(s) (fasta or fastq, gzipped or not) and a set of input sequences (starters).<\/p>\n<!-- Time to render link large description section of link id 23935: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23935: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23935: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/www.netlab.uky.edu\/p\/bioinfo\/MapSplice\" id=\"link-23660\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MapSplice<\/a>\n<!-- Time to render name section of link id 23660: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Accurate mapping of RNA-seq reads for splice junction discovery.<\/p>\n<!-- Time to render link large description section of link id 23660: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23660: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23660: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/www.staff.ncl.ac.uk\/richard.howey\/mapthin\/\" id=\"link-24365\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MapThin<\/a>\n<!-- Time to render name section of link id 24365: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Reduce the number of SNPs in a gene marker dense map computed by PLINK. First, by eliminating linked SNPs. Then, by applying different criteria.<\/p>\n<!-- Time to render link large description section of link id 24365: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24365: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24365: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/schloi\/MARVEL\" id=\"link-23888\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MARVEL<\/a>\n<!-- Time to render name section of link id 23888: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.<\/p>\n<!-- Time to render link large description section of link id 23888: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23888: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23888: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/LaboratorioBioinformatica\/MARVEL\" id=\"link-24366\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MARVEL_bins<\/a>\n<!-- Time to render name section of link id 24366: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MARVEL (Metagenomic Analysis and Retrieval of Viral Elements) is a tool for recovery of draft phage genomes from whole community shotgun metagenomic sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24366: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24366: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24366: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/Mash\" id=\"link-25098\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mash<\/a>\n<!-- Time to render name section of link id 25098: 3.0994415283203E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25098: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Mash> How to use <\/a>\n<!-- Time to render notes section of link id 25098: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25098: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/Mash\" id=\"link-25099\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mash<\/a>\n<!-- Time to render name section of link id 25099: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Fast genome and metagenome distance estimation using MinHash.<\/p>\r\n<p>documentation : <a href=\"https:\/\/mash.readthedocs.io\/en\/latest\/\">Publications \u2014 Mash 2.0 documentation<\/a><\/p>\n<!-- Time to render link large description section of link id 25099: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Mash> How to use <\/a>\n<!-- Time to render notes section of link id 25099: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25099: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/MashMap\" id=\"link-24367\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MashMap<\/a>\n<!-- Time to render name section of link id 24367: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. \u00a0It can be useful for mapping genome assembly or long reads (PacBio\/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, Mashmap computes alignment boundaries and identity estimates using\u00a0k-mers. It does not compute the alignments explicitly, but rather estimates a\u00a0k-mer based\u00a0Jaccard similarity\u00a0using a combination of\u00a0Minimizers\u00a0and\u00a0MinHash. This is then converted to an estimate of sequence identity using the\u00a0Mash distance.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24367: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24367: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24367: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/lskatz\/mashtree\" id=\"link-24993\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mashtree<\/a>\n<!-- Time to render name section of link id 24993: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Create a tree using Mash distances.<\/p>\n<!-- Time to render link large description section of link id 24993: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mashtree> How to use <\/a>\n<!-- Time to render notes section of link id 24993: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24993: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/www.genome.umd.edu\/masurca.html\" id=\"link-23661\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MaSuRCA<\/a>\n<!-- Time to render name section of link id 23661: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MaSuRCA is whole genome assembly software. It combines the efficiency of the de\u00a0Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454)<\/p>\n<!-- Time to render link large description section of link id 23661: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MaSuRCA> How to use <\/a>\n<!-- Time to render notes section of link id 23661: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23661: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/matchap\/\" id=\"link-24368\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAtCHap<\/a>\n<!-- Time to render name section of link id 24368: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An ultra fast algorithm for solving the single individual haplotype assembly problem.<\/p>\n<!-- Time to render link large description section of link id 24368: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24368: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24368: 0.00019097328186035 --> \n<tr><td><a href=\"http:\/\/darlinglab.org\/mauve\/mauve.html\" id=\"link-23662\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mauve<\/a>\n<!-- Time to render name section of link id 23662: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics.\u00a0 Aligning whole genomes is a fundamentally different problem than aligning short sequences.<\/p>\n<!-- Time to render link large description section of link id 23662: 0 --> \n<\/td>\n<td>><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Mauve> How to use <\/a>\n<!-- Time to render notes section of link id 23662: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23662: 0.00019311904907227 --> \n<tr><td><a href=\"https:\/\/downloads.jbei.org\/data\/microbial_communities\/MaxBin\/MaxBin.html\" id=\"link-23861\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MaxBin2<\/a>\n<!-- Time to render name section of link id 23861: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.<\/p>\n<!-- Time to render link large description section of link id 23861: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23861: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23861: 0.00016379356384277 --> \n<tr><td><a href=\"https:\/\/github.com\/al-mcintyre\/mCaller\" id=\"link-24063\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mCaller<\/a>\n<!-- Time to render name section of link id 24063: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This program is designed to call m6A from nanopore data using the differences between measured and expected currents.<\/p>\n<!-- Time to render link large description section of link id 24063: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24063: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24063: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/GonzalezLab\/MCHelper\" id=\"link-25758\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MCHelper<\/a>\n<!-- Time to render name section of link id 25758: 2.8610229492188E-6 --> \n<\/td>\n<td><p>An automatic tool to curate transposable element libraries.<\/p>\n<!-- Time to render link large description section of link id 25758: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MCHelper> How to use <\/a>\n<!-- Time to render notes section of link id 25758: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25758: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/micans.org\/mcl\/\" id=\"link-23919\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MCL<\/a>\n<!-- Time to render name section of link id 23919: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.<\/p>\n<!-- Time to render link large description section of link id 23919: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MCL> How to use <\/a>\n<!-- Time to render notes section of link id 23919: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23919: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/github.com\/wyp1125\/MCScanX\" id=\"link-24369\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MCScanX<\/a>\n<!-- Time to render name section of link id 24369: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MCScan is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors.<\/p>\n<!-- Time to render link large description section of link id 24369: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MCScanX> How to use <\/a>\n<!-- Time to render notes section of link id 24369: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24369: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/MECAT\" id=\"link-23979\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MECAT<\/a>\n<!-- Time to render name section of link id 23979: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads.<\/p>\n<!-- Time to render link large description section of link id 23979: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23979: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23979: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/medaka\" id=\"link-23989\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Medaka<\/a>\n<!-- Time to render name section of link id 23989: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Medaka demonstrates a framework for error correcting sequencing data, particularly aimed at nanopore sequencing. Tools are provided for both training and inference. The code exploits the keras deep learning library.<\/p>\n<!-- Time to render link large description section of link id 23989: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Medaka> How to use <\/a>\n<!-- Time to render notes section of link id 23989: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23989: 0.00020289421081543 --> \n<tr><td><a href=\"https:\/\/www.megasoftware.net\/\" id=\"link-24370\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEGA-CC<\/a>\n<!-- Time to render name section of link id 24370: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software suite for analyzing DNA and protein sequence data from species and populations.<\/p>\n<!-- Time to render link large description section of link id 24370: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24370: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24370: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/github.com\/voutcn\/megahit\" id=\"link-23780\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEGAHIT<\/a>\n<!-- Time to render name section of link id 23780: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph<\/p>\n<!-- Time to render link large description section of link id 23780: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MEGAHIT> How to use <\/a>\n<!-- Time to render notes section of link id 23780: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23780: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/megalodon\" id=\"link-24129\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Megalodon<\/a>\n<!-- Time to render name section of link id 24129: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Megalodon provides \"basecalling augmentation\" for raw nanopore sequencing reads, including direct, reference-guided SNP and modified base calling.<\/p>\n<!-- Time to render link large description section of link id 24129: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24129: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24129: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/LANL-Bioinformatics\/MeGAMerge\" id=\"link-23925\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MeGAMerge<\/a>\n<!-- Time to render name section of link id 23925: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool to merge assembled contigs, long reads from metagenomic sequencing runs<\/p>\n<!-- Time to render link large description section of link id 23925: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23925: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23925: 0.00016117095947266 --> \n<tr><td><a href=\"http:\/\/www-ab.informatik.uni-tuebingen.de\/software\/megan\/welcome.html\" id=\"link-23663\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEGAN<\/a>\n<!-- Time to render name section of link id 23663: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MEtaGenome ANalyzer : Metagenomic data analysis : taxonomic and functionnal (SEED and KEGG classification) analysis.\u00a0<\/p>\n<!-- Time to render link large description section of link id 23663: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MEGAN> How to use <\/a>\n<!-- Time to render notes section of link id 23663: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23663: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/xff.cz\/megatools\/\" id=\"link-25681\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MegaTools<\/a>\n<!-- Time to render name section of link id 25681: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Open-source command line tools for accessing Mega.co.nz cloud storage.<\/p>\n<!-- Time to render link large description section of link id 25681: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Megatools> How to use <\/a>\n<!-- Time to render notes section of link id 25681: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25681: 0.00017285346984863 --> \n<tr><td><a href=\"http:\/\/meme-suite.org\/\" id=\"link-23664\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEME<\/a>\n<!-- Time to render name section of link id 23664: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The MEME Suite allows you to: (1)&amp;nbspdiscover motifs using MEME or GLAM2 on groups of related DNA or protein sequences, (2)&amp;nbspsearch sequence databases using motifs, (3)&amp;nbspcompare a motif to all motifs in a database of motifs, and (3)&amp;nbspassociate motifs with Gene Ontology terms via their putative target genes.<\/p>\n<!-- Time to render link large description section of link id 23664: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MEME> How to use <\/a>\n<!-- Time to render notes section of link id 23664: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23664: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/github.com\/arangrhie\/merfin\" id=\"link-24371\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Merfin<\/a>\n<!-- Time to render name section of link id 24371: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Evaluate variant calls and its combination with k-mer multiplicity.<\/p>\n<!-- Time to render link large description section of link id 24371: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24371: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24371: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/www.stavrox.com\/\" id=\"link-25970\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MeroX<\/a>\n<!-- Time to render name section of link id 25970: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MeroX is based on StavroX. It is specialized for cleavable cross-linkers. In addition to peptide backbone fragments, MeroX identifies cross-linker specific fragments in MS-MS data.<\/p>\n<!-- Time to render link large description section of link id 25970: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MeroX> How to use <\/a>\n<!-- Time to render notes section of link id 25970: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25970: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/merqury\" id=\"link-24372\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Merqury<\/a>\n<!-- Time to render name section of link id 24372: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Evaluate genome assemblies with k-mers and more<\/p>\n<!-- Time to render link large description section of link id 24372: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Merqury> How to use <\/a>\n<!-- Time to render notes section of link id 24372: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24372: 0.00018215179443359 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/meryl\" id=\"link-24373\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Meryl<\/a>\n<!-- Time to render name section of link id 24373: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A genomic k-mer counter (and sequence utility) with nice features.<\/p>\n<!-- Time to render link large description section of link id 24373: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Meryl> How to use <\/a>\n<!-- Time to render notes section of link id 24373: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24373: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/metexplore\/met4j\" id=\"link-24713\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Met4j<\/a>\n<!-- Time to render name section of link id 24713: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.<\/p>\n<!-- Time to render link large description section of link id 24713: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24713: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24713: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/berkeleylab\/metabat\/src\/master\/\" id=\"link-24374\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaBat<\/a>\n<!-- Time to render name section of link id 24374: 2.8610229492188E-6 --> \n<\/td>\n<td><p>An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24374: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24374: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24374: 0.00016283988952637 --> \n<tr><td><a href=\"https:\/\/github.com\/envmetagen\/metabinkit\" id=\"link-25994\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">metabinkit<\/a>\n<!-- Time to render name section of link id 25994: 2.8610229492188E-6 --> \n<\/td>\n<td><p>From metagenomic or metabarcoding data, it is often necessary to assign taxonomy to DNA sequences. This is generally performed by aligning sequences to a reference database, usually resulting in multiple database alignments for each query sequence. Using these alignment results, metabinkit assigns a single taxon to each query sequence, based on user-defined percentage identity thresholds. In essence, for each query, the alignments are filtered based on the percentage identity thresholds and the lowest common ancestor for all alignments passing the filters is determined. The metabin program is not limited to BLAST alignments, and can accept alignment results produced using any program, provided the input format is correct. However, functionality is also available to create BLAST databases and to perform BLAST alignments, which can be passed directly to metabin.<\/p>\n<!-- Time to render link large description section of link id 25994: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_metabinkit> How to use <\/a>\n<!-- Time to render notes section of link id 25994: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25994: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/Glouvel\/metabit\" id=\"link-23941\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">metaBIT<\/a>\n<!-- Time to render name section of link id 23941: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.<\/p>\n<!-- Time to render link large description section of link id 23941: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_metaBIT> How to use <\/a>\n<!-- Time to render notes section of link id 23941: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23941: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/AnantharamanLab\/METABOLIC\/wiki\/METABOLIC-Usage\" id=\"link-26226\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">METABOLIC<\/a>\n<!-- Time to render name section of link id 26226: 2.1457672119141E-6 --> \n<\/td>\n<td><p>METabolic And BiogeOchemistry anaLyses In miCrobes<\/p>\n<!-- Time to render link large description section of link id 26226: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_METABOLIC> How to use <\/a>\n<!-- Time to render notes section of link id 26226: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26226: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/metaDMG-dev\/metaDMG-core\" id=\"link-25336\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">metaDMG<\/a>\n<!-- Time to render name section of link id 25336: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A fast and accurate ancient DNA damage toolkit for metagenomic data.<\/p>\n<!-- Time to render link large description section of link id 25336: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_metaDMG> How to use <\/a>\n<!-- Time to render notes section of link id 25336: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25336: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/metaeuk\" id=\"link-24375\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaEuk<\/a>\n<!-- Time to render name section of link id 24375: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.<\/p>\n<!-- Time to render link large description section of link id 24375: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaEuk> How to use <\/a>\n<!-- Time to render notes section of link id 24375: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24375: 0.00017786026000977 --> \n<tr><td><a href=\"http:\/\/csg.sph.umich.edu\/abecasis\/metal\/index.html\" id=\"link-23994\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">METAL<\/a>\n<!-- Time to render name section of link id 23994: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.<\/p>\n<!-- Time to render link large description section of link id 23994: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23994: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23994: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/DiltheyLab\/MetaMaps\" id=\"link-23971\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaMaps<\/a>\n<!-- Time to render name section of link id 23971: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MetaMaps is tool specifically developed for the analysis of long-read (PacBio\/ONT) metagenomic datasets. It simultaenously carries out read assignment and sample composition estimation. It is faster than classical exact alignment-based approaches, and its output is more information-rich than that of kmer-spectra-based methods. For example, each MetaMaps alignment comes with an approximate alignment location, an estimated alignment identity and a mapping quality.<\/p>\n<!-- Time to render link large description section of link id 23971: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23971: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23971: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/GaetanBenoitDev\/metaMDBG\" id=\"link-25473\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaMDBG<\/a>\n<!-- Time to render name section of link id 25473: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A lightweight assembler for long and accurate metagenomics reads.<\/p>\n<!-- Time to render link large description section of link id 25473: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaMDBG> How to use <\/a>\n<!-- Time to render notes section of link id 25473: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25473: 0.00020718574523926 --> \n<tr><td><a href=\"https:\/\/github.com\/biobakery\/MetaPhlAn\" id=\"link-24798\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn<\/a>\n<!-- Time to render name section of link id 24798: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24798: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaPhlAn> How to use <\/a>\n<!-- Time to render notes section of link id 24798: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24798: 0.00017189979553223 --> \n<tr><td><a href=\"https:\/\/github.com\/biobakery\/metaphlan\" id=\"link-23665\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn2<\/a>\n<!-- Time to render name section of link id 23665: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MetaPhlAn2 is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.<\/p>\n<!-- Time to render link large description section of link id 23665: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaPhlAn> How to use <\/a>\n<!-- Time to render notes section of link id 23665: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23665: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/biobakery\/MetaPhlAn\/tree\/3.0\" id=\"link-24376\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn3<\/a>\n<!-- Time to render name section of link id 24376: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.<\/p>\n<!-- Time to render link large description section of link id 24376: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24376: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24376: 0.00021719932556152 --> \n<tr><td><a href=\"https:\/\/huttenhower.sph.harvard.edu\/metaphlan\/\" id=\"link-25176\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn4<\/a>\n<!-- Time to render name section of link id 25176: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling.<\/p>\n<!-- Time to render link large description section of link id 25176: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaPhlAn> How to use <\/a>\n<!-- Time to render notes section of link id 25176: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25176: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/bxlab\/metaWRAP\" id=\"link-24377\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaWRAP<\/a>\n<!-- Time to render name section of link id 24377: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A flexible pipeline for genome-resolved metagenomic data analysis.<\/p>\n<!-- Time to render link large description section of link id 24377: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaWRAP> How to use <\/a>\n<!-- Time to render notes section of link id 24377: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24377: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/microbiology.se\/software\/metaxa2\/\" id=\"link-24378\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Metaxa2<\/a>\n<!-- Time to render name section of link id 24378: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.<\/p>\n<!-- Time to render link large description section of link id 24378: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Metaxa2> How to use <\/a>\n<!-- Time to render notes section of link id 24378: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24378: 0.00018787384033203 --> \n<tr><td><a href=\"https:\/\/github.com\/abardet\/methylasso\" id=\"link-25475\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MethyLasso<\/a>\n<!-- Time to render name section of link id 25475: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole-genome datasets.<\/p>\n<!-- Time to render link large description section of link id 25475: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MethyLasso> How to use <\/a>\n<!-- Time to render notes section of link id 25475: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25475: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/dpryan79\/MethylDackel\" id=\"link-25055\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MethylDackel<\/a>\n<!-- Time to render name section of link id 25055: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.<\/p>\n<!-- Time to render link large description section of link id 25055: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MethylDackel> How to use <\/a>\n<!-- Time to render notes section of link id 25055: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25055: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/methylKit.html\" id=\"link-24379\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">methylKit<\/a>\n<!-- Time to render name section of link id 24379: 3.0994415283203E-6 --> \n<\/td>\n<td><p>DNA methylation analysis from high-throughput bisulfite sequencing results<\/p>\n<!-- Time to render link large description section of link id 24379: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24379: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24379: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/Computomics\/\" id=\"link-24711\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MethylScore<\/a>\n<!-- Time to render name section of link id 24711: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Identification of differentially methylated regions between multiple epigenomes from BS-treated read mappings via methylated region calling.<\/p>\n<!-- Time to render link large description section of link id 24711: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MethylScore> How to use <\/a>\n<!-- Time to render notes section of link id 24711: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24711: 0.00019383430480957 --> \n<tr><td><a href=\"https:\/\/github.com\/MontrealCorpusTools\/Montreal-Forced-Aligner\" id=\"link-25976\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MFA<\/a>\n<!-- Time to render name section of link id 25976: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The Montreal Forced Aligner is a command line utility for performing forced alignment of speech datasets using Kaldi (http:\/\/kaldi-asr.org\/).<\/p>\n<!-- Time to render link large description section of link id 25976: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MFA> How to use <\/a>\n<!-- Time to render notes section of link id 25976: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25976: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/caleblareau\/mgatk\" id=\"link-25397\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mgatk<\/a>\n<!-- Time to render name section of link id 25397: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A mitochondrial genome analysis toolkit.<\/p>\n<!-- Time to render link large description section of link id 25397: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mgatk> How to use <\/a>\n<!-- Time to render notes section of link id 25397: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25397: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/bpucker\/MGSE\" id=\"link-24120\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MGSE<\/a>\n<!-- Time to render name section of link id 24120: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly.<\/p>\n<!-- Time to render link large description section of link id 24120: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24120: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24120: 0.00017881393432617 --> \n<tr><td><a href=\"https:\/\/github.com\/mamba-org\/micromamba-releases\" id=\"link-26230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">micromamba<\/a>\n<!-- Time to render name section of link id 26230: 1.7881393432617E-5 --> \n<\/td>\n<td><p>micromamba is a single-file executable that is statically linked and can be dropped anywhere on the operating to get started with powerful package management and virtual environments.<\/p>\n<!-- Time to render link large description section of link id 26230: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_micromamba> How to use <\/a>\n<!-- Time to render notes section of link id 26230: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26230: 0.00018787384033203 --> \n<tr><td><a href=\"https:\/\/kimura.univ-montp2.fr\/~rousset\/Migraine.htm\" id=\"link-26085\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Migraine<\/a>\n<!-- Time to render name section of link id 26085: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Migraine implements coalescent algorithms for maximum likelihood analysis of population genetic data. It considers Allelic counts and DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 26085: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Migraine> How to use <\/a>\n<!-- Time to render notes section of link id 26085: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26085: 0.00018215179443359 --> \n<tr><td><a href=\"https:\/\/peterbeerli.com\/migrate-html5\/index.html\" id=\"link-25550\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Migrate<\/a>\n<!-- Time to render name section of link id 25550: 2.8610229492188E-6 --> \n<\/td>\n<td>Migrate estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture.\n<!-- Time to render link large description section of link id 25550: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Migrate> How to use <\/a>\n<!-- Time to render notes section of link id 25550: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25550: 0.00018477439880371 --> \n<tr><td><a href=\"https:\/\/github.com\/thh32\/MiMiC2\" id=\"link-26236\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiMiC2<\/a>\n<!-- Time to render name section of link id 26236: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MiMiC2 is a bioinformatic pipeline for the selection of a few microbial genomes that functionally represent an entire ecosystem, termed a synthetic community (SynCom).<\/p>\n<!-- Time to render link large description section of link id 26236: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MiMiC2> How to use <\/a>\n<!-- Time to render notes section of link id 26236: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26236: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/ctSkennerton\/minced\/\" id=\"link-23666\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MinCED<\/a>\n<!-- Time to render name section of link id 23666: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the command-line and was derived from CRT<\/p>\n<!-- Time to render link large description section of link id 23666: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23666: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23666: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/miniasm\" id=\"link-23810\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniasm<\/a>\n<!-- Time to render name section of link id 23810: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Ultrafast de novo assembly for long noisy reads (though having no consensus step).<\/p>\n<!-- Time to render link large description section of link id 23810: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniasm> How to use <\/a>\n<!-- Time to render notes section of link id 23810: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23810: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/calacademy-research\/minibar\" id=\"link-25619\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">minibar<\/a>\n<!-- Time to render name section of link id 25619: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Dual barcode and primer demultiplexing for MinION sequenced reads.<\/p>\n<!-- Time to render link large description section of link id 25619: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_minibar> How to use <\/a>\n<!-- Time to render notes section of link id 25619: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25619: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/conda-forge\/miniforge\" id=\"link-25642\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniforge<\/a>\n<!-- Time to render name section of link id 25642: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Miniforge is a minimal installer for Conda specific to conda-forge.<\/p>\n<!-- Time to render link large description section of link id 25642: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniforge> How to use <\/a>\n<!-- Time to render notes section of link id 25642: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25642: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/minigraph\" id=\"link-24381\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minigraph<\/a>\n<!-- Time to render name section of link id 24381: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Minigraph is a sequence-to-graph mapper and graph constructor.<\/p>\n<!-- Time to render link large description section of link id 24381: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minigraph> How to use <\/a>\n<!-- Time to render notes section of link id 24381: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24381: 0.00016093254089355 --> \n<tr><td><a href=\"https:\/\/github.com\/statgen\/Minimac4\/\" id=\"link-24382\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minimac4<\/a>\n<!-- Time to render name section of link id 24382: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality.<\/p>\n<!-- Time to render link large description section of link id 24382: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minimac4> How to use <\/a>\n<!-- Time to render notes section of link id 24382: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24382: 0.00020503997802734 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/minimap\" id=\"link-23811\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minimap<\/a>\n<!-- Time to render name section of link id 23811: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Experimental tool to find approximate mapping positions between long sequences<\/p>\n<!-- Time to render link large description section of link id 23811: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minimap> How to use <\/a>\n<!-- Time to render notes section of link id 23811: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23811: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/roblanf\/minion_qc\" id=\"link-24383\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MinIONQC<\/a>\n<!-- Time to render name section of link id 24383: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast and effective quality control for MinION and PromethION sequencing data<\/p>\n<!-- Time to render link large description section of link id 24383: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24383: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24383: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Minipolish\" id=\"link-24384\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minipolish<\/a>\n<!-- Time to render name section of link id 24384: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool for Racon polishing of miniasm assemblies.<\/p>\n<!-- Time to render link large description section of link id 24384: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minipolish> How to use <\/a>\n<!-- Time to render notes section of link id 24384: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24384: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/miniprot\" id=\"link-24385\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniprot<\/a>\n<!-- Time to render name section of link id 24385: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Aligning proteins to genomes with splicing and frameshift.<\/p>\n<!-- Time to render link large description section of link id 24385: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniprot> How to use <\/a>\n<!-- Time to render notes section of link id 24385: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24385: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/berkeleylab\/jgi-miniscrub\/src\/master\/\" id=\"link-24386\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiniScrub<\/a>\n<!-- Time to render name section of link id 24386: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MiniScrub is a de novo long sequencing read preprocessing method that improves read quality by predicting and removing (\"scrubbing\") read segments that have a high concentration of errors.<\/p>\n<!-- Time to render link large description section of link id 24386: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24386: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24386: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/shendurelab\/MIPGEN\" id=\"link-25501\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MIPgen<\/a>\n<!-- Time to render name section of link id 25501: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Use MIPgen to design custom mip panels for target enrichment of moderate to high complexity DNA targets ranging from 120 to 250bp in size.<\/p>\n<!-- Time to render link large description section of link id 25501: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MIPgen> How to use <\/a>\n<!-- Time to render notes section of link id 25501: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25501: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/mira-assembler\" id=\"link-23667\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MIRA<\/a>\n<!-- Time to render name section of link id 23667: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Whole genome shotgun and EST sequence assembler for Sanger, 454, and Solexa \/ Illumina.<\/p>\n<!-- Time to render link large description section of link id 23667: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MIRA> How to use <\/a>\n<!-- Time to render notes section of link id 23667: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23667: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/www.mdc-berlin.de\/n-rajewsky#t-data,software&#038;resources\" id=\"link-23668\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">miRDeep2<\/a>\n<!-- Time to render name section of link id 23668: 3.0994415283203E-6 --> \n<\/td>\n<td><p>miRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples. Last, a new module for preprocessing of raw Illumina sequencing data produces files for downstream analysis with the miRDeep2 or quantifier module.<\/p>\n<!-- Time to render link large description section of link id 23668: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_miRDeep2> How to use <\/a>\n<!-- Time to render notes section of link id 23668: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23668: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/wwwabi.snv.jussieu.fr\/research\/publi\/small_ncRNA\/\" id=\"link-23875\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiRfold<\/a>\n<!-- Time to render name section of link id 23875: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MiRfold searches for a good miRNA-like folding in the sequence surrounding a putative miRNA. It was optimized on plant miRNAs.<\/p>\n<!-- Time to render link large description section of link id 23875: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23875: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23875: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/pedronachtigall\/MITGARD\" id=\"link-24674\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MITGARD<\/a>\n<!-- Time to render name section of link id 24674: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MITGARD (Mitochondrial Genome Assembly from RNA-seq Data) is a computational tool designed to recover the mitochondrial genome from RNA-seq data of any Eukaryote species.<\/p>\n<!-- Time to render link large description section of link id 24674: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MITGARD> How to use <\/a>\n<!-- Time to render notes section of link id 24674: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24674: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/chrishah\/MITObim\" id=\"link-24387\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MITObim<\/a>\n<!-- Time to render name section of link id 24387: 1.0013580322266E-5 --> \n<\/td>\n<td><p>The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads.<\/p>\n<!-- Time to render link large description section of link id 24387: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MITObim> How to use <\/a>\n<!-- Time to render notes section of link id 24387: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24387: 0.00037789344787598 --> \n<tr><td><a href=\"https:\/\/github.com\/dpuiu\/MitoHPC\" id=\"link-25224\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoHPC<\/a>\n<!-- Time to render name section of link id 25224: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MitoHPC : Mitochondrial High Performance Caller. For Calling Mitochondrial Homoplasmies and Heteroplasmies.<\/p>\n<!-- Time to render link large description section of link id 25224: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoHPC> How to use <\/a>\n<!-- Time to render notes section of link id 25224: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25224: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/riverlee\/MitoSeek\" id=\"link-24390\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoSeek<\/a>\n<!-- Time to render name section of link id 24390: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.<\/p>\n<!-- Time to render link large description section of link id 24390: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24390: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24390: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/linzhi2013\/MitoZ\" id=\"link-24392\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoZ<\/a>\n<!-- Time to render name section of link id 24392: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization.<\/p>\n<!-- Time to render link large description section of link id 24392: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoZ> How to use <\/a>\n<!-- Time to render notes section of link id 24392: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24392: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/KCCG\/mity\" id=\"link-25760\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mity<\/a>\n<!-- Time to render name section of link id 25760: 2.1457672119141E-6 --> \n<\/td>\n<td>A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data \n<!-- Time to render link large description section of link id 25760: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mity> How to use <\/a>\n<!-- Time to render notes section of link id 25760: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25760: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/mlst\" id=\"link-24394\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MLST<\/a>\n<!-- Time to render name section of link id 24394: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Multi-Locus sequence Typing. The method enables investigators to determine the ST based on WGS data.<\/p>\n<!-- Time to render link large description section of link id 24394: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24394: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24394: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/mzytnicki\/mmannot\" id=\"link-24395\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mmannot<\/a>\n<!-- Time to render name section of link id 24395: 2.8610229492188E-6 --> \n<\/td>\n<td><p>mmannot annotates reads, or quantifies the features. For instance, suppose that you have sequenced your organism of interest with sRNA-Seq (RNA-Seq works too), and you want to know how many times you have sequenced miRNAs, rRNAs, tRNAs, etc. This is what mmannot does. A huge proportion of the reads may actually map at several locations. These multi-mapping reads are usually handled poorly by similar quantification tools. In our methods, when a read maps at several locations, all these locations are inspected: If all these locations belong to the same feature (e.g. miRNAs, in case of a duplicated gene family), the read is still annotated as a miRNA. If the location belong to different features (e.g. 3'UTR and miRNA), the read is ambiguous, and is flagged as 3'UTR--miRNA. In case 1, we say when have\u00a0rescued\u00a0a read.<\/p>\n<!-- Time to render link large description section of link id 24395: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24395: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24395: 0.00018787384033203 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/mzytnicki\/multi-mapping-counter\/overview\" id=\"link-23965\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mmquant<\/a>\n<!-- Time to render name section of link id 23965: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This tool counts the number of reads (produced by RNA-Seq) per gene, much like HTSeq-count and featureCounts. The main difference with other tools is that multi-mapping reads are counted differently: if a read is mapped to gene A, gene B, and gene C, the tool will create a new feature, \"geneA--geneB--geneC\", that will be counted once.<\/p>\n<!-- Time to render link large description section of link id 23965: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mmquant> How to use <\/a>\n<!-- Time to render notes section of link id 23965: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23965: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/MMseqs2\" id=\"link-24097\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MMseqs2<\/a>\n<!-- Time to render name section of link id 24097: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge proteins\/nucleotide sequence sets.<\/p>\n<!-- Time to render link large description section of link id 24097: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MMseqs2> How to use <\/a>\n<!-- Time to render notes section of link id 24097: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24097: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/phac-nml\/mob-suite\" id=\"link-26168\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MOB-suite<\/a>\n<!-- Time to render name section of link id 26168: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.<\/p>\r\n<p>The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.<\/p>\n<!-- Time to render link large description section of link id 26168: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MOB-suite> How to use <\/a>\n<!-- Time to render notes section of link id 26168: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26168: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/mhkj\/mge_finder\" id=\"link-24396\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MobileElementFinder<\/a>\n<!-- Time to render name section of link id 24396: 7.8678131103516E-6 --> \n<\/td>\n<td><p>MobileElementFinder is a tool for identifying Mobile Genetic Elements (MGEs) in Whole Genome Shotgun sequence data.<\/p>\n<!-- Time to render link large description section of link id 24396: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MobileElementFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24396: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24396: 0.00054597854614258 --> \n<tr><td><a href=\"https:\/\/github.com\/jyhehir\/mobster\" id=\"link-23669\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mobster<\/a>\n<!-- Time to render name section of link id 23669: 7.8678131103516E-6 --> \n<\/td>\n<td><p>Mobster is used to detect novel (non-reference) Mobile Element Insertion (MEI) events in BAM files and uses both a discordant read pair method and a split-read method.<\/p>\n<!-- Time to render link large description section of link id 23669: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23669: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23669: 0.00052499771118164 --> \n<tr><td><a href=\"https:\/\/github.com\/epi2me-labs\/modbam2bed\" id=\"link-24714\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">modbam2bed<\/a>\n<!-- Time to render name section of link id 24714: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.<\/p>\n<!-- Time to render link large description section of link id 24714: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_modbam2bed> How to use <\/a>\n<!-- Time to render notes section of link id 24714: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24714: 0.00031900405883789 --> \n<tr><td><a href=\"https:\/\/github.com\/ddarriba\/modeltest\" id=\"link-24001\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ModelTest-NG<\/a>\n<!-- Time to render name section of link id 24001: 7.8678131103516E-6 --> \n<\/td>\n<td><p>ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.<\/p>\n<!-- Time to render link large description section of link id 24001: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ModelTest-NG> How to use <\/a>\n<!-- Time to render notes section of link id 24001: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24001: 0.00055313110351562 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/modkit\" id=\"link-25325\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Modkit<\/a>\n<!-- Time to render name section of link id 25325: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics.<\/p>\n<!-- Time to render link large description section of link id 25325: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Modkit> How to use <\/a>\n<!-- Time to render notes section of link id 25325: 1.9073486328125E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25325: 0.00060296058654785 --> \n<tr><td><a href=\"https:\/\/code.google.com\/p\/mosaik-aligner\/\" id=\"link-23670\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MOSAIK<\/a>\n<!-- Time to render name section of link id 23670: 7.1525573730469E-6 --> \n<\/td>\n<td><p><strong>MOSAIK<\/strong> is a reference-guided assembler comprising of two main modular programs<\/p>\n<!-- Time to render link large description section of link id 23670: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23670: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23670: 0.00053000450134277 --> \n<tr><td><a href=\"https:\/\/github.com\/brentp\/mosdepth\" id=\"link-24065\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mosdepth<\/a>\n<!-- Time to render name section of link id 24065: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Fast BAM\/CRAM depth calculation for WGS, exome, or targeted sequencing. mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome. mean per-window depth given a window size--as would be used for CNV calling. the mean per-region given a BED file of regions. a distribution of proportion of bases covered at or above a given threshhold for each chromosome and genome-wide. quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20) threshold output to indicate how many bases in each region are covered at the given thresholds. when appropriate, the output files are bgzipped and indexed for ease of use.<\/p>\n<!-- Time to render link large description section of link id 24065: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mosdepth> How to use <\/a>\n<!-- Time to render notes section of link id 24065: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24065: 0.00054502487182617 --> \n<tr><td><a href=\"http:\/\/www.mothur.org\/wiki\/Main_Page\" id=\"link-23671\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mothur<\/a>\n<!-- Time to render name section of link id 23671: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The one-stop source for your computational microbial ecology needs. mothur offers the ability to go from raw sequences to the generation of visualization tools to describe alpha and beta diversity.<\/p>\n<!-- Time to render link large description section of link id 23671: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mothur> How to use <\/a>\n<!-- Time to render notes section of link id 23671: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23671: 0.00054788589477539 --> \n<tr><td><a href=\"https:\/\/github.com\/Pas-Kapli\/mptp\" id=\"link-24397\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mPTP<\/a>\n<!-- Time to render name section of link id 24397: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A tool for single-locus species delimitation.<\/p>\n<!-- Time to render link large description section of link id 24397: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mPTP> How to use <\/a>\n<!-- Time to render notes section of link id 24397: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24397: 0.00042104721069336 --> \n<tr><td><a href=\"http:\/\/mrbayes.sourceforge.net\/\" id=\"link-23672\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MrBayes<\/a>\n<!-- Time to render name section of link id 23672: 4.0531158447266E-6 --> \n<\/td>\n<td><p>MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.<\/p>\n<!-- Time to render link large description section of link id 23672: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MrBayes> How to use <\/a>\n<!-- Time to render notes section of link id 23672: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23672: 0.00024509429931641 --> \n<tr><td><a href=\"http:\/\/mreps.univ-mlv.fr\" id=\"link-24398\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mreps<\/a>\n<!-- Time to render name section of link id 24398: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Software for tandem repeat identification in DNA.<\/p>\n<!-- Time to render link large description section of link id 24398: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mreps> How to use <\/a>\n<!-- Time to render notes section of link id 24398: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24398: 0.00025510787963867 --> \n<tr><td><a href=\"http:\/\/home.uchicago.edu\/rhudson1\/source\/mksamples.html\" id=\"link-23673\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ms<\/a>\n<!-- Time to render name section of link id 23673: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A program for generating samples under neutral models.<\/p>\n<!-- Time to render link large description section of link id 23673: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ms> How to use <\/a>\n<!-- Time to render notes section of link id 23673: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23673: 0.00028800964355469 --> \n<tr><td><a href=\"https:\/\/github.com\/arumugamlab\/msamtools\" id=\"link-26027\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msamtools<\/a>\n<!-- Time to render name section of link id 26027: 3.0994415283203E-6 --> \n<\/td>\n<td><p>msamtools provides useful functions that are commonly used in microbiome data analysis, especially when analyzing shotgun metagenomics or metatranscriptomics data.<\/p>\n<!-- Time to render link large description section of link id 26027: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msamtools> How to use <\/a>\n<!-- Time to render notes section of link id 26027: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26027: 0.00022602081298828 --> \n<tr><td><a href=\"http:\/\/msbayes.sourceforge.net\/\" id=\"link-23947\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msBayes<\/a>\n<!-- Time to render name section of link id 23947: 1.9073486328125E-6 --> \n<\/td>\n<td><p>msBayes allows complex and flexible comparative phylogeographic inference.<\/p>\n<!-- Time to render link large description section of link id 23947: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23947: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23947: 0.00016593933105469 --> \n<tr><td><a href=\"https:\/\/github.com\/nunofonseca\/msi\" id=\"link-24399\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MSI<\/a>\n<!-- Time to render name section of link id 24399: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MSI was designed for sequencing reads with higher error rates (e.g., as the ones produced by Nanopore's sequencers) but also works with reads with lower error rates (e.g., Illumina).<\/p>\n<!-- Time to render link large description section of link id 24399: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24399: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24399: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/xjtu-omics\/msisensor-pro\" id=\"link-25252\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MSIsensor-pro<\/a>\n<!-- Time to render name section of link id 25252: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25252: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MSIsensor-pro> How to use <\/a>\n<!-- Time to render notes section of link id 25252: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25252: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/github.com\/stschiff\/msmc\" id=\"link-23674\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msmc<\/a>\n<!-- Time to render name section of link id 23674: 4.0531158447266E-6 --> \n<\/td>\n<td><p>This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences<\/p>\n<!-- Time to render link large description section of link id 23674: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msmc> How to use <\/a>\n<!-- Time to render notes section of link id 23674: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23674: 0.00021886825561523 --> \n<tr><td><a href=\"https:\/\/github.com\/stschiff\/msmc2\" id=\"link-23799\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msmc2<\/a>\n<!-- Time to render name section of link id 23799: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data<\/p>\n<!-- Time to render link large description section of link id 23799: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msmc2> How to use <\/a>\n<!-- Time to render notes section of link id 23799: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23799: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/Genometric\/MSPC\/\" id=\"link-25674\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MSPC<\/a>\n<!-- Time to render name section of link id 25674: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Improve Sensitivity and Specificity of Peak Calling, and Identify Consensus Regions<\/p>\n<!-- Time to render link large description section of link id 25674: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MSPC> How to use <\/a>\n<!-- Time to render notes section of link id 25674: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25674: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/tskit-dev\/msprime\" id=\"link-25085\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msprime<\/a>\n<!-- Time to render name section of link id 25085: 4.0531158447266E-6 --> \n<\/td>\n<td><p dir=\"auto\"><code>msprime<\/code>\u00a0is a population genetics simulator based on\u00a0<a href=\"https:\/\/tskit.dev\/\" rel=\"nofollow\">tskit<\/a>. Msprime can simulate random ancestral histories for a sample of individuals (consistent with a given demographic model) under a range of different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral history (which can be produced by msprime or other programs supporting\u00a0<a href=\"https:\/\/tskit.dev\/\" rel=\"nofollow\">tskit<\/a>) under a variety of genome sequence evolution models.<\/p>\r\n<p dir=\"auto\">Please see the\u00a0<a href=\"https:\/\/tskit.dev\/msprime\/docs\/latest\/\" rel=\"nofollow\">documentation<\/a>\u00a0for more details<\/p>\n<!-- Time to render link large description section of link id 25085: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msprime> How to use <\/a>\n<!-- Time to render notes section of link id 25085: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25085: 0.00035500526428223 --> \n<tr><td><a href=\"https:\/\/github.com\/mhinsch\/msums\" id=\"link-24061\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msums<\/a>\n<!-- Time to render name section of link id 24061: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A program for the efficient computation of a number of population genetics summary statistics. msums can read ms-format data on (nearly) arbitrary numbers of populations.<\/p>\n<!-- Time to render link large description section of link id 24061: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24061: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24061: 0.00024700164794922 --> \n<tr><td><a href=\"https:\/\/github.com\/anne-gcd\/MTG-Link\" id=\"link-24400\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MTG-Link<\/a>\n<!-- Time to render name section of link id 24400: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MTG-Link is a novel gap-filling tool for draft genome assemblies, dedicated to linked read data.<\/p>\n<!-- Time to render link large description section of link id 24400: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24400: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24400: 0.00026512145996094 --> \n<tr><td><a href=\"http:\/\/mugsy.sourceforge.net\/\" id=\"link-24401\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mugsy<\/a>\n<!-- Time to render name section of link id 24401: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome. Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 2011 27(3):334-4<\/p>\n<!-- Time to render link large description section of link id 24401: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Mugsy> How to use <\/a>\n<!-- Time to render notes section of link id 24401: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24401: 0.00023102760314941 --> \n<tr><td><a href=\"http:\/\/multalin.toulouse.inra.fr\/multalin\/multalin.html\" id=\"link-23675\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MultAlin<\/a>\n<!-- Time to render name section of link id 23675: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Multiple sequence alignment <a name=\"sequence_input_format\"><\/a>with hierarchical clustering.<b><\/b><\/p>\n<!-- Time to render link large description section of link id 23675: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23675: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23675: 0.00026488304138184 --> \n<tr><td><a href=\"http:\/\/multiqc.info\/\" id=\"link-23822\" class=\"track_this_link \" rel=\"noopener noreferrer\">MultiQC<\/a>\n<!-- Time to render name section of link id 23822: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Aggregate results from bioinformatics analyses across many samples into a single report.<\/p>\n<!-- Time to render link large description section of link id 23822: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MultiQC> How to use <\/a>\n<!-- Time to render notes section of link id 23822: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23822: 0.00023198127746582 --> \n<tr><td><a href=\"https:\/\/github.com\/mummer4\/mummer\" id=\"link-23676\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MUMmer<\/a>\n<!-- Time to render name section of link id 23676: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MUMmer is a package for rapidly aligning <b>entire genomes<\/b>, whether in complete or draft form.<\/p>\n<!-- Time to render link large description section of link id 23676: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MUMmer> How to use <\/a>\n<!-- Time to render notes section of link id 23676: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23676: 0.00023603439331055 --> \n<tr><td><a href=\"http:\/\/genome.gsc.riken.jp\/osc\/english\/dataresource\/\" id=\"link-24402\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MuMRescueLite<\/a>\n<!-- Time to render name section of link id 24402: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MuMRescueLite is the software that enable to use the tag sequencies of mapped to multiple loci to the genome, for the expression analysis. At the mapping of short sequence tags of CAGE or ChIP-Seq to the genome, sequence tags that map to multiple genomic loci (multi-mapping tags or MuMs), are routinely omitted from further analysis, leading to experimental bias and reduced coverage. MuMRescueLite probabilistically reincorporates multi-mapping tags into mapped short read data with acceptable computational requirements.<\/p>\n<!-- Time to render link large description section of link id 24402: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24402: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24402: 0.00022387504577637 --> \n<tr><td><a href=\"http:\/\/www.drive5.com\/muscle\/\" id=\"link-23677\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MUSCLE<\/a>\n<!-- Time to render name section of link id 23677: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Multiple sequence alignment (nucleic or proteic).<\/p>\n<!-- Time to render link large description section of link id 23677: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MUSCLE> How to use <\/a>\n<!-- Time to render notes section of link id 23677: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23677: 0.00023102760314941 --> \n<tr><td><a href=\"http:\/\/musket.sourceforge.net\/homepage.htm#latest\" id=\"link-24403\" class=\"track_this_link \" rel=\"noopener noreferrer\">Musket<\/a>\n<!-- Time to render name section of link id 24403: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing.<\/p>\n<!-- Time to render link large description section of link id 24403: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24403: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24403: 0.00025200843811035 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/ccoclet\/mvp\" id=\"link-25282\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MVP<\/a>\n<!-- Time to render name section of link id 25282: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MVP stands for Multi-choice Viromics Pipeline. It is a simplified pipeline that utilizes a suite of state-of-art tools to easily get from a set of contigs to a vOTU heatmap (and more).<\/p>\n<!-- Time to render link large description section of link id 25282: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MVP> How to use <\/a>\n<!-- Time to render notes section of link id 25282: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25282: 0.00023794174194336 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/sb2nhri\/files\/MyCC\/\" id=\"link-23915\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MyCC<\/a>\n<!-- Time to render name section of link id 23915: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.<\/p>\n<!-- Time to render link large description section of link id 23915: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23915: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23915: 0.00022387504577637 --> \n<tr><td><a href=\"https:\/\/github.com\/bluenote-1577\/myloasm\" id=\"link-25993\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">myloasm<\/a>\n<!-- Time to render name section of link id 25993: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Myloasm is a de novo metagenome assembler for long-read sequencing data. It takes sequencing reads and outputs polished contigs in a single command.<\/p>\n<!-- Time to render link large description section of link id 25993: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_myloasm> How to use <\/a>\n<!-- Time to render notes section of link id 25993: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25993: 0.00024199485778809 --> \n<tr><td><a href=\"http:\/\/mzmine.github.io\" id=\"link-25243\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MZmine<\/a>\n<!-- Time to render name section of link id 25243: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MZmine is an open-source software for mass-spectrometry data processing.<\/p>\n<!-- Time to render link large description section of link id 25243: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MZmine> How to use <\/a>\n<!-- Time to render notes section of link id 25243: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25243: 0.00025701522827148 --> \n<tr><td><a href=\"http:\/\/www.ks.uiuc.edu\/Research\/namd\/\" id=\"link-23678\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NAMD<\/a>\n<!-- Time to render name section of link id 23678: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.<\/p>\n<!-- Time to render link large description section of link id 23678: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NAMD> How to use <\/a>\n<!-- Time to render notes section of link id 23678: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23678: 0.00025606155395508 --> \n<tr><td><a href=\"https:\/\/github.com\/PrestonLeung\/Nano-Q\" id=\"link-24405\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Nano-Q<\/a>\n<!-- Time to render name section of link id 24405: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Python script for conservatively cleaning ONT reads from bam files and estimate variant frequencies.<\/p>\n<!-- Time to render link large description section of link id 24405: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24405: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24405: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/ImagoXV\/NanoASV\/tree\/main\" id=\"link-25782\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoASV<\/a>\n<!-- Time to render name section of link id 25782: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Nanopore full-length 16S metabarcoding amplicon data analysis<\/p>\n<!-- Time to render link large description section of link id 25782: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoASV> How to use <\/a>\n<!-- Time to render notes section of link id 25782: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25782: 0.00026488304138184 --> \n<tr><td><a href=\"https:\/\/github.com\/WGLab\/NanoCaller\" id=\"link-24406\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCaller<\/a>\n<!-- Time to render name section of link id 24406: 3.814697265625E-6 --> \n<\/td>\n<td><p>NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs\/indels from long-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24406: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoCaller> How to use <\/a>\n<!-- Time to render notes section of link id 24406: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24406: 0.00028610229492188 --> \n<tr><td><a href=\"https:\/\/github.com\/genomicsITER\/NanoCLUST\" id=\"link-24407\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCLUST<\/a>\n<!-- Time to render name section of link id 24407: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads.<\/p>\n<!-- Time to render link large description section of link id 24407: 0.00020790100097656 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoCLUST> How to use <\/a>\n<!-- Time to render notes section of link id 24407: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24407: 0.00037884712219238 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoComp\" id=\"link-23942\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoComp<\/a>\n<!-- Time to render name section of link id 23942: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Compare multiple runs of long read sequencing data and alignments.<\/p>\n<!-- Time to render link large description section of link id 23942: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.11.1\n<!-- Time to render notes section of link id 23942: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23942: 0.00037193298339844 --> \n<tr><td><a href=\"https:\/\/github.com\/a-slide\/NanoCount\" id=\"link-24408\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCount<\/a>\n<!-- Time to render name section of link id 24408: 7.8678131103516E-6 --> \n<\/td>\n<td><p>NanoCount estimates transcripts abundance from Oxford Nanopore direct-RNA sequencing datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads.<\/p>\n<!-- Time to render link large description section of link id 24408: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24408: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24408: 0.0005490779876709 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/nanofilt\" id=\"link-23857\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoFilt<\/a>\n<!-- Time to render name section of link id 23857: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Filtering and trimming of Oxford Nanopore sequencing data<\/p>\n<!-- Time to render link large description section of link id 23857: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23857: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23857: 0.00055098533630371 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoLyse\" id=\"link-23944\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoLyse<\/a>\n<!-- Time to render name section of link id 23944: 6.1988830566406E-6 --> \n<\/td>\n<td><p>Remove reads mapping to the lambda phage genome from a fastq file<\/p>\n<!-- Time to render link large description section of link id 23944: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_nanolyse> How to use <\/a>\n<!-- Time to render notes section of link id 23944: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23944: 0.00042009353637695 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoPlot\" id=\"link-23855\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoPlot<\/a>\n<!-- Time to render name section of link id 23855: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Plotting tool for Oxford Nanopore sequencing data and alignments.<\/p>\n<!-- Time to render link large description section of link id 23855: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoPlot> How to use <\/a>\n<!-- Time to render notes section of link id 23855: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23855: 0.00042080879211426 --> \n<tr><td><a href=\"https:\/\/github.com\/jts\/nanopolish\" id=\"link-23823\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Nanopolish<\/a>\n<!-- Time to render name section of link id 23823: 5.9604644775391E-6 --> \n<\/td>\n<td><p>A nanopore consensus algorithm using a signal-level hidden Markov model. Signal-level algorithms for MinION data.<\/p>\n<!-- Time to render link large description section of link id 23823: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Nanopolish> How to use <\/a>\n<!-- Time to render notes section of link id 23823: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23823: 0.00043392181396484 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/NanoSim\" id=\"link-24029\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoSim<\/a>\n<!-- Time to render name section of link id 24029: 5.9604644775391E-6 --> \n<\/td>\n<td><p>NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology.<\/p>\n<!-- Time to render link large description section of link id 24029: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoSim> How to use <\/a>\n<!-- Time to render notes section of link id 24029: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24029: 0.00042319297790527 --> \n<tr><td><a href=\"https:\/\/nanospc.mmmoxford.uk\" id=\"link-24409\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoSPC<\/a>\n<!-- Time to render name section of link id 24409: 8.1062316894531E-6 --> \n<\/td>\n<td><p>NanoSPC is a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24409: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoSPC> How to use <\/a>\n<!-- Time to render notes section of link id 24409: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24409: 0.000579833984375 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoStat\" id=\"link-23943\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoStat<\/a>\n<!-- Time to render name section of link id 23943: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Create statistic summary of an Oxford Nanopore read dataset<\/p>\n<!-- Time to render link large description section of link id 23943: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoStat> How to use <\/a>\n<!-- Time to render notes section of link id 23943: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23943: 0.0005958080291748 --> \n<tr><td><a href=\"http:\/\/www.genoscope.cns.fr\/externe\/nas\/\" id=\"link-23990\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NaS<\/a>\n<!-- Time to render name section of link id 23990: 6.9141387939453E-6 --> \n<\/td>\n<td><p>NaS is a hybrid approach developed to take advantage of data generated using MinION device. It combines Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads<\/p>\n<!-- Time to render link large description section of link id 23990: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23990: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23990: 0.00052785873413086 --> \n<tr><td><a href=\"https:\/\/github.com\/SethMMorton\/natsort\" id=\"link-24410\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">natsort<\/a>\n<!-- Time to render name section of link id 24410: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Simple yet flexible natural sorting in Python<\/p>\n<!-- Time to render link large description section of link id 24410: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24410: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24410: 0.00051498413085938 --> \n<tr><td><a href=\"http:\/\/blast.ncbi.nlm.nih.gov\" id=\"link-23679\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_Blast<\/a>\n<!-- Time to render name section of link id 23679: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Similarity search against databanks.<\/p>\n<!-- Time to render link large description section of link id 23679: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_Blast> How to use <\/a>\n<!-- Time to render notes section of link id 23679: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23679: 0.00051784515380859 --> \n<tr><td><a href=\"http:\/\/blast.ncbi.nlm.nih.gov\" id=\"link-23868\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_Blast+<\/a>\n<!-- Time to render name section of link id 23868: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Similarity search against databanks.<\/p>\n<!-- Time to render link large description section of link id 23868: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_Blast+> How to use <\/a>\n<!-- Time to render notes section of link id 23868: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23868: 0.00049686431884766 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/datasets\" id=\"link-25057\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_datasets<\/a>\n<!-- Time to render name section of link id 25057: 7.1525573730469E-6 --> \n<\/td>\n<td><p>NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. You can use it to find and download sequence, annotation, and metadata for genes and genomes using our command-line interface (CLI) tools or\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/\" rel=\"nofollow\">NCBI Datasets<\/a>\u00a0web interface.<\/p>\n<!-- Time to render link large description section of link id 25057: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_datasets> How to use <\/a>\n<!-- Time to render notes section of link id 25057: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25057: 0.00052595138549805 --> \n<tr><td><a href=\"ftp:\/\/ftp.ncbi.nih.gov\/toolbox\/ncbi_tools\/\" id=\"link-23886\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_tools<\/a>\n<!-- Time to render name section of link id 23886: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NCBI portable software toolkit<\/p>\n<!-- Time to render link large description section of link id 23886: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_tools> How to use <\/a>\n<!-- Time to render notes section of link id 23886: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23886: 0.00019216537475586 --> \n<tr><td><a href=\"ftp:\/\/ftp.ncbi.nih.gov\/toolbox\/ncbi_tools++\/\" id=\"link-23895\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_tools++<\/a>\n<!-- Time to render name section of link id 23895: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NCBI C++ Toolkit provides free, portable, public domain libraries.<\/p>\n<!-- Time to render link large description section of link id 23895: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_tools++> How to use <\/a>\n<!-- Time to render notes section of link id 23895: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23895: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/NECAT\" id=\"link-24411\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NECAT<\/a>\n<!-- Time to render name section of link id 24411: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.<\/p>\n<!-- Time to render link large description section of link id 24411: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NECAT> How to use <\/a>\n<!-- Time to render notes section of link id 24411: 0.0011007785797119 --> \n<\/td><\/tr>\n<!-- Time to render link id 24411: 0.0016570091247559 --> \n<tr><td><a href=\"https:\/\/ccl.northwestern.edu\/netlogo\/\" id=\"link-24412\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NetLogo<\/a>\n<!-- Time to render name section of link id 24412: 6.9141387939453E-6 --> \n<\/td>\n<td><p>NetLogo is a multi-agent programmable modeling environment.<\/p>\n<!-- Time to render link large description section of link id 24412: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24412: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24412: 0.00053215026855469 --> \n<tr><td><a href=\"https:\/\/github.com\/AI-sandbox\/neural-admixture\" id=\"link-25021\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Neural-ADMIXTURE<\/a>\n<!-- Time to render name section of link id 25021: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Neural ADMIXTURE is an unsupervised global ancestry inference technique based on ADMIXTURE. By using neural networks, Neural ADMIXTURE offers high quality ancestry assignments with a running time which is much faster than ADMIXTURE's.<\/p>\n<!-- Time to render link large description section of link id 25021: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Neural-ADMIXTURE> How to use <\/a>\n<!-- Time to render notes section of link id 25021: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25021: 0.00052809715270996 --> \n<tr><td><a href=\"http:\/\/en.wikipedia.org\/wiki\/Newbler\" id=\"link-23680\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Newbler<\/a>\n<!-- Time to render name section of link id 23680: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche diagnostic.<\/p>\n<!-- Time to render link large description section of link id 23680: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23680: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23680: 0.00052499771118164 --> \n<tr><td><a href=\"http:\/\/cegg.unige.ch\/newick_utils\" id=\"link-24083\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Newick_Utilities<\/a>\n<!-- Time to render name section of link id 24083: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees. We distribute the package under the BSD License. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).<\/p>\n<!-- Time to render link large description section of link id 24083: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Newick_Utilities> How to use <\/a>\n<!-- Time to render notes section of link id 24083: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24083: 0.00049781799316406 --> \n<tr><td><a href=\"https:\/\/docs.nextcloud.com\/desktop\/3.4\/advancedusage.html\" id=\"link-24413\" class=\"track_this_link \" rel=\"noopener noreferrer\">NextCloudcmd<\/a>\n<!-- Time to render name section of link id 24413: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A command line client that can be used to synchronize Nextcloud files to client machines.<\/p>\n<!-- Time to render link large description section of link id 24413: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24413: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24413: 0.0002751350402832 --> \n<tr><td><a href=\"https:\/\/github.com\/Nextomics\/NextDenovo\" id=\"link-24414\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NextDenovo<\/a>\n<!-- Time to render name section of link id 24414: 4.0531158447266E-6 --> \n<\/td>\n<td><p>NextDenovo is a string graph-based de novo assembler for TGS long reads.<\/p>\n<!-- Time to render link large description section of link id 24414: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextDenovo> How to use <\/a>\n<!-- Time to render notes section of link id 24414: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24414: 0.00027203559875488 --> \n<tr><td><a href=\"https:\/\/www.nextflow.io\/\" id=\"link-23889\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Nextflow<\/a>\n<!-- Time to render name section of link id 23889: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.<\/p>\n<!-- Time to render link large description section of link id 23889: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Nextflow> How to use <\/a>\n<!-- Time to render notes section of link id 23889: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23889: 0.00027298927307129 --> \n<tr><td><a href=\"https:\/\/github.com\/Nextomics\/NextPolish\" id=\"link-24415\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NextPolish<\/a>\n<!-- Time to render name section of link id 24415: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NextPolish is used to fix base errors (SNV\/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both.<\/p>\n<!-- Time to render link large description section of link id 24415: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextPolish> How to use <\/a>\n<!-- Time to render notes section of link id 24415: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24415: 0.00027203559875488 --> \n<tr><td><a href=\"https:\/\/github.com\/nf-core\/\" id=\"link-24009\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nf-core workflows<\/a>\n<!-- Time to render name section of link id 24009: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This module provide access to workflows nf-core, there are automatically downloaded into your home.<\/p>\r\n<p><strong>More info at <a href=\"https:\/\/github.com\/nf-core\/configs\/blob\/master\/docs\/genotoul.md\">nf-core\/config<\/a> page.<\/strong><\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 24009: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextflowWorkflows> How to use <\/a>\n<!-- Time to render notes section of link id 24009: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24009: 0.00028586387634277 --> \n<tr><td><a href=\"https:\/\/github.com\/philres\/ngmlr\" id=\"link-24037\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NGMLR<\/a>\n<!-- Time to render name section of link id 24037: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations SV detection from paired end reads mapping<\/p>\n<!-- Time to render link large description section of link id 24037: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NGMLR> How to use <\/a>\n<!-- Time to render notes section of link id 24037: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24037: 0.00028681755065918 --> \n<tr><td><a href=\"https:\/\/github.com\/fgvieira\/ngsLD\" id=\"link-24728\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsLD<\/a>\n<!-- Time to render name section of link id 24728: 3.814697265625E-6 --> \n<\/td>\n<td><p>ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account.<\/p>\n<!-- Time to render link large description section of link id 24728: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ngsLD> How to use <\/a>\n<!-- Time to render notes section of link id 24728: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24728: 0.00028491020202637 --> \n<tr><td><a href=\"https:\/\/github.com\/ANGSD\/NgsRelate\" id=\"link-23867\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsRelate<\/a>\n<!-- Time to render name section of link id 23867: 5.0067901611328E-6 --> \n<\/td>\n<td><p>NgsRelate can be used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.<\/p>\n<!-- Time to render link large description section of link id 23867: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NgsRelate> How to use <\/a>\n<!-- Time to render notes section of link id 23867: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23867: 0.00028681755065918 --> \n<tr><td><a href=\"https:\/\/github.com\/mfumagalli\/ngsTools\" id=\"link-23681\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsTools<\/a>\n<!-- Time to render name section of link id 23681: 3.814697265625E-6 --> \n<\/td>\n<td><p><b>ngsTools<\/b> is a collection of programs for population genetics analyses from NGS data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data.<\/p>\n<!-- Time to render link large description section of link id 23681: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ngsTools> How to use <\/a>\n<!-- Time to render notes section of link id 23681: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23681: 0.0003049373626709 --> \n<tr><td><a href=\"https:\/\/ngsutils.org\" id=\"link-24675\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsutils<\/a>\n<!-- Time to render name section of link id 24675: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Tools for next-generation sequencing analysis.<\/p>\n<!-- Time to render link large description section of link id 24675: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NGSUtils> How to use <\/a>\n<!-- Time to render notes section of link id 24675: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24675: 0.00029397010803223 --> \n<tr><td><a href=\"https:\/\/github.com\/TravisWheelerLab\/NINJA\" id=\"link-24416\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NINJA<\/a>\n<!-- Time to render name section of link id 24416: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Nearly Infinite Neighbor Joining Application<\/p>\n<!-- Time to render link large description section of link id 24416: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NINJA> How to use <\/a>\n<!-- Time to render notes section of link id 24416: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24416: 0.00018787384033203 --> \n<tr><td><a href=\"https:\/\/github.com\/steuernb\/NLR-Annotator\" id=\"link-24417\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NLR-Annotator<\/a>\n<!-- Time to render name section of link id 24417: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. NLR-Annotator is a tool to annotate loci associated with NLRs in large sequences.<\/p>\n<!-- Time to render link large description section of link id 24417: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24417: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24417: 0.00020885467529297 --> \n<tr><td><a href=\"https:\/\/github.com\/slt666666\/NLRtracker\" id=\"link-25307\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NLRtracker<\/a>\n<!-- Time to render name section of link id 25307: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NLRtracker extracts and functionally annotates NLRs from protein or transcript files based on the core features found in the RefPlantNLR dataset.<\/p>\n<!-- Time to render link large description section of link id 25307: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NLRtracker> How to use <\/a>\n<!-- Time to render notes section of link id 25307: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25307: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/abcsFrederick\/non-B_gfa\" id=\"link-24418\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">non-B_gfa<\/a>\n<!-- Time to render name section of link id 24418: 1.9073486328125E-6 --> \n<\/td>\n<td><p>gfa programs for Non-B site at NCI\/FNLCR. gfa is a Suite of programs developed at NCI-Frederick\/Frederick National Lab to find sequences associated with non-B DNA forming motifs.<\/p>\n<!-- Time to render link large description section of link id 24418: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24418: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24418: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/ndierckx\/NOVOLoci\" id=\"link-26077\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NOVOLoci<\/a>\n<!-- Time to render name section of link id 26077: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NOVOLoci is a haplotype aware assembler for targeted assembly or whole genome assembly of small genomes.\u00a0<\/p>\r\n<p dir=\"auto\">We currently recommend limiting the assembly size to regions &lt;20 Mb in targeted-mode and diploid genomes that are &lt;250 Mb in WG-mode, with a minimum sequencing depth of 10x per haplotype.<\/p>\r\n<p dir=\"auto\">If you do need to phase accuratly and you have HiFi or R10 ONT data, it is adviced to use Hifiasm, as it is has a much shorter runtime.<\/p>\r\n<p>Currently it is only available for Nanopore, PacBio and hybrid options will be available soon.<\/p>\n<!-- Time to render link large description section of link id 26077: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NOVOLoci> How to use <\/a>\n<!-- Time to render notes section of link id 26077: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26077: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/ndierckx\/NOVOPlasty\" id=\"link-24055\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NOVOPlasty<\/a>\n<!-- Time to render name section of link id 24055: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NOVOPlasty is a de novo assembler and variance caller for short circular genomes.<\/p>\n<!-- Time to render link large description section of link id 24055: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NOVOPlasty> How to use <\/a>\n<!-- Time to render notes section of link id 24055: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24055: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/OmarOakheart\/nPhase\" id=\"link-24419\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nPhase<\/a>\n<!-- Time to render name section of link id 24419: 3.0994415283203E-6 --> \n<\/td>\n<td><p>nPhase is a ploidy agnostic tool developed in python which predicts the haplotypes of a sample that was sequenced by both long and short reads by aligning them to a reference. It should work with any ploidy.<\/p>\n<!-- Time to render link large description section of link id 24419: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24419: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24419: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/clwgg\/nQuire\" id=\"link-24420\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nQuire<\/a>\n<!-- Time to render name section of link id 24420: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A statistical framework for ploidy estimation using NGS short-read data.<\/p>\n<!-- Time to render link large description section of link id 24420: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_nQuire> How to use <\/a>\n<!-- Time to render notes section of link id 24420: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24420: 0.00016403198242188 --> \n<tr><td><a href=\"ftp:\/\/ftp.ncbi.nih.gov\/pub\/seg\/nseg\/\" id=\"link-23923\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NSEG<\/a>\n<!-- Time to render name section of link id 23923: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NSEG is used to mask nucleic acid sequences, needed by RepeatScout.<\/p>\n<!-- Time to render link large description section of link id 23923: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NSEG> How to use <\/a>\n<!-- Time to render notes section of link id 23923: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23923: 0.0001838207244873 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ntEdit\" id=\"link-24421\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ntEdit<\/a>\n<!-- Time to render name section of link id 24421: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ntEdit is a fast and scalable genomics application for polishing genome assembly drafts. It simplifies polishing and \"haploidization\" of gene and genome sequences with its re-usable Bloom filter design.<\/p>\n<!-- Time to render link large description section of link id 24421: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24421: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24421: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ntHits\" id=\"link-24422\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ntHits<\/a>\n<!-- Time to render name section of link id 24422: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ntHits is a method for identifying reapeats in high-throughput DNA sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24422: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24422: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24422: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ntjoin\" id=\"link-24423\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ntJoin<\/a>\n<!-- Time to render name section of link id 24423: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Scaffolding draft assemblies using reference assemblies and minimizer graphs<\/p>\n<!-- Time to render link large description section of link id 24423: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ntJoin> How to use <\/a>\n<!-- Time to render notes section of link id 24423: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24423: 0.00018405914306641 --> \n<tr><td><a href=\"http:\/\/numpy.scipy.org\/\" id=\"link-23682\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">numpy<\/a>\n<!-- Time to render name section of link id 23682: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NumPy is a package needed for scientific computing with Python.<\/p>\n<!-- Time to render link large description section of link id 23682: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23682: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23682: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/dzerbino\/oases\" id=\"link-23683\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Oases<\/a>\n<!-- Time to render name section of link id 23683: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz). <br \/>\r\n<br \/>\r\nOases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.<\/p>\n<!-- Time to render link large description section of link id 23683: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Oases> How to use <\/a>\n<!-- Time to render notes section of link id 23683: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23683: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/c-zhou\/oatk\" id=\"link-25662\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">oatk<\/a>\n<!-- Time to render name section of link id 25662: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A organelle de novo genome assembly toolkit. (Install include OatkDB)<\/p>\n<!-- Time to render link large description section of link id 25662: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Oatk> How to use <\/a>\n<!-- Time to render notes section of link id 25662: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25662: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/obitools\/wikis\/home\" id=\"link-23910\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OBITools<\/a>\n<!-- Time to render name section of link id 23910: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OBITools is a set of python programs developed to simplify the manipulation of sequence files in our labs. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.<\/p>\n<!-- Time to render link large description section of link id 23910: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OBITools> How to use <\/a>\n<!-- Time to render notes section of link id 23910: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23910: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/pangenome\/odgi\" id=\"link-24424\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">odgi<\/a>\n<!-- Time to render name section of link id 24424: 2.8610229492188E-6 --> \n<\/td>\n<td><p>odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses.<\/p>\n<!-- Time to render link large description section of link id 24424: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_odgi> How to use <\/a>\n<!-- Time to render notes section of link id 24424: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24424: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/omabrowser.org\/standalone\/\" id=\"link-24753\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OMA<\/a>\n<!-- Time to render name section of link id 24753: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The OMA (Orthologous MAtrix) database is a well-established resource for identifying orthologs among publicly available complete genomes.<\/p>\n<!-- Time to render link large description section of link id 24753: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OMA> How to use <\/a>\n<!-- Time to render notes section of link id 24753: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24753: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/github.com\/DessimozLab\/OMArk\" id=\"link-25541\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OMArk<\/a>\n<!-- Time to render name section of link id 25541: 1.9073486328125E-6 --> \n<\/td>\n<td><p>OMArk is a software for proteome (protein-coding gene repertoire) quality assessment.<\/p>\n<!-- Time to render link large description section of link id 25541: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OMArk> How to use <\/a>\n<!-- Time to render notes section of link id 25541: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25541: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/TF-Chan-Lab\/OMBlast\" id=\"link-24004\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OMBlast<\/a>\n<!-- Time to render name section of link id 24004: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An alignment tool for optical mapping data.<\/p>\n<!-- Time to render link large description section of link id 24004: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24004: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24004: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/alachins\/omegaplus\" id=\"link-24425\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">omegaplus<\/a>\n<!-- Time to render name section of link id 24425: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A scalable tool for rapid detection of selective sweeps in whole-genome datasets.<\/p>\n<!-- Time to render link large description section of link id 24425: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OmegaPlus> How to use <\/a>\n<!-- Time to render notes section of link id 24425: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24425: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/doua.prabi.fr\/software\/one-code-to-find-them-all\" id=\"link-24426\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Onecodetofindthemall<\/a>\n<!-- Time to render name section of link id 24426: 3.0994415283203E-6 --> \n<\/td>\n<td><p>One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information.<\/p>\n<!-- Time to render link large description section of link id 24426: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24426: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24426: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/ont_fast5_api\" id=\"link-24086\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ont_fast5_api<\/a>\n<!-- Time to render name section of link id 24086: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore fast5 file format.<\/p>\n<!-- Time to render link large description section of link id 24086: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ont_fast5_api> How to use <\/a>\n<!-- Time to render notes section of link id 24086: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24086: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/openbabel.org\/\" id=\"link-26150\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OpenBabel<\/a>\n<!-- Time to render name section of link id 26150: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Open Babel is a chemical toolbox designed to speak the many languages of chemical data.<\/p>\n<!-- Time to render link large description section of link id 26150: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OpenBabel> How to use <\/a>\n<!-- Time to render notes section of link id 26150: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26150: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/github.com\/aqlaboratory\/openfold-3\" id=\"link-26159\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Openfold3<\/a>\n<!-- Time to render name section of link id 26159: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fully open source biomolecular structure prediction model based on AlphaFold3.<\/p>\n<!-- Time to render link large description section of link id 26159: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Openfold3> How to use <\/a>\n<!-- Time to render notes section of link id 26159: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26159: 0.00016117095947266 --> \n<tr><td><a href=\"https:\/\/github.com\/audeering\/opensmile-python\" id=\"link-25646\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">openSMILE<\/a>\n<!-- Time to render name section of link id 25646: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Python package for openSMILE (open-source Speech and Music Interpretation by Large-space Extraction).<\/p>\n<!-- Time to render link large description section of link id 25646: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_openSMILE> How to use <\/a>\n<!-- Time to render notes section of link id 25646: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25646: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/pseudogene\/ora\" id=\"link-23959\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ORA<\/a>\n<!-- Time to render name section of link id 23959: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 40kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functional with DNA and EST sequence, no intron supported.<\/p>\n<!-- Time to render link large description section of link id 23959: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23959: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23959: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/orffinder\/\" id=\"link-24427\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ORFfinder<\/a>\n<!-- Time to render name section of link id 24427: 2.8610229492188E-6 --> \n<\/td>\n<td><p>ORFfinder searches for open reading frames (ORFs) in the DNA sequence you enter.<\/p>\n<!-- Time to render link large description section of link id 24427: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ORFfinder> How to use <\/a>\n<!-- Time to render notes section of link id 24427: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24427: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/org-asm\/org-asm\" id=\"link-24106\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ORG.asm<\/a>\n<!-- Time to render name section of link id 24106: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The ORGanelle ASseMbler aims to target the assembling of small sequences over-represented in a whole genome shotgun sequence dataset.<\/p>\n<!-- Time to render link large description section of link id 24106: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ORG.Asm> How to use <\/a>\n<!-- Time to render notes section of link id 24106: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24106: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/aubombarely\/Organelle_PBA\" id=\"link-24429\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Organelle_PBA<\/a>\n<!-- Time to render name section of link id 24429: 1.9073486328125E-6 --> \n<\/td>\n<td><p>OrganelleRef_PBA is a script to perform a de-novo PacBio assemblies of any organelle (chloroplast or mitochondrial genomes) using several programs.<\/p>\n<!-- Time to render link large description section of link id 24429: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24429: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24429: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/orthagogue\/\" id=\"link-23968\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">orthAgogue<\/a>\n<!-- Time to render name section of link id 23968: 1.9073486328125E-6 --> \n<\/td>\n<td><p>a tool for high speed estimation of homology relations within and between species in massive data sets. orthAgogue is easy to use and offers flexibility through a range of optional parameters.<\/p>\n<!-- Time to render link large description section of link id 23968: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23968: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23968: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/davidemms\/OrthoFinder\" id=\"link-23920\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OrthoFinder<\/a>\n<!-- Time to render name section of link id 23920: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.<\/p>\n<!-- Time to render link large description section of link id 23920: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OrthoFinder> How to use <\/a>\n<!-- Time to render notes section of link id 23920: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23920: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/orthologer.ezlab.org\/#getting-orthologer-software\" id=\"link-24775\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OrthoLoger<\/a>\n<!-- Time to render name section of link id 24775: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Standalone pipeline for delineation of orthologs.<\/p>\n<!-- Time to render link large description section of link id 24775: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24775: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24775: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/orthomcl.org\" id=\"link-24681\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OrthoMCL<\/a>\n<!-- Time to render name section of link id 24681: 1.9073486328125E-6 --> \n<\/td>\n<td><p>OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.<\/p>\n<!-- Time to render link large description section of link id 24681: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OrthoMCL> How to use <\/a>\n<!-- Time to render notes section of link id 24681: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24681: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/swarris\/Pacasus\" id=\"link-24006\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pacasus<\/a>\n<!-- Time to render name section of link id 24006: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Tool for detecting and cleaning PacBio \/ Nanopore long reads after whole genome amplification.<\/p>\n<!-- Time to render link large description section of link id 24006: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24006: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24006: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/open2c\/pairtools\" id=\"link-25323\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pairtools<\/a>\n<!-- Time to render name section of link id 25323: 1.9073486328125E-6 --> \n<\/td>\n<td><p>pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment.<\/p>\n<!-- Time to render link large description section of link id 25323: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pairtools> How to use <\/a>\n<!-- Time to render notes section of link id 25323: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25323: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/MikkelSchubert\/paleomix\/wiki\/Overview\" id=\"link-23684\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PALEOMIX<\/a>\n<!-- Time to render name section of link id 23684: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The PALEOMIX pipeline is a set of free and open-source pipelines and tools designed to enable the rapid processing of Next Generation Sequencing (NGS) data, starting from de-multiplexed reads from one or more samples, through sequence processing and alignment, and ending with genotyping, phylogenetic inference on the samples, as well as metagenomic analysis of the samples.<\/p>\n<!-- Time to render link large description section of link id 23684: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PALEOMIX> How to use <\/a>\n<!-- Time to render notes section of link id 23684: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23684: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/rcedgar\/palm_annot\" id=\"link-25761\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">palm_annot<\/a>\n<!-- Time to render name section of link id 25761: 3.0994415283203E-6 --> \n<\/td>\n<td>Scripts, HMMs and search databases for identifying and classifying viral RdRp sequences \n<!-- Time to render link large description section of link id 25761: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_palm_annot> How to use <\/a>\n<!-- Time to render notes section of link id 25761: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25761: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/rcedgar\/palmscan\" id=\"link-25921\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Palmscan<\/a>\n<!-- Time to render name section of link id 25921: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Palmscan is software to detect viral polymerase palmprint barcode sequences in longer sequences such as virus genomes and ORFs. Palmprints can be used to classify RNA viruses.<\/p>\n<!-- Time to render link large description section of link id 25921: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Palmscan> How to use <\/a>\n<!-- Time to render notes section of link id 25921: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25921: 0.00019311904907227 --> \n<tr><td><a href=\"http:\/\/abacus.gene.ucl.ac.uk\/software\/paml.html\" id=\"link-23685\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PAML<\/a>\n<!-- Time to render name section of link id 23685: 8.1062316894531E-6 --> \n<\/td>\n<td><p>PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.<\/p>\n<!-- Time to render link large description section of link id 23685: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PAML> How to use <\/a>\n<!-- Time to render notes section of link id 23685: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23685: 0.00053191184997559 --> \n<tr><td><a href=\"https:\/\/github.com\/gem-pasteur\/PanACoTA\" id=\"link-26201\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanACoTA<\/a>\n<!-- Time to render name section of link id 26201: 7.8678131103516E-6 --> \n<\/td>\n<td><p>PANgenome with Annotations, COre identification, Tree and corresponding Alignments.<\/p>\n<!-- Time to render link large description section of link id 26201: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanACoTA> How to use <\/a>\n<!-- Time to render notes section of link id 26201: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26201: 0.00053000450134277 --> \n<tr><td><a href=\"https:\/\/github.com\/marschall-lab\/panacus\" id=\"link-25448\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">panacus<\/a>\n<!-- Time to render name section of link id 25448: 6.9141387939453E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25448: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_panacus> How to use <\/a>\n<!-- Time to render notes section of link id 25448: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25448: 0.00052404403686523 --> \n<tr><td><a href=\"http:\/\/pandoc.org\/\" id=\"link-23808\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pandoc<\/a>\n<!-- Time to render name section of link id 23808: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.<\/p>\n<!-- Time to render link large description section of link id 23808: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pandoc> How to use <\/a>\n<!-- Time to render notes section of link id 23808: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23808: 0.00047802925109863 --> \n<tr><td><a href=\"https:\/\/github.com\/eblerjana\/pangenie\" id=\"link-24960\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanGenie<\/a>\n<!-- Time to render name section of link id 24960: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph.<\/p>\n<!-- Time to render link large description section of link id 24960: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanGenie> How to use <\/a>\n<!-- Time to render notes section of link id 24960: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24960: 0.00045585632324219 --> \n<tr><td><a href=\"https:\/\/github.com\/piosierra\/pantera\" id=\"link-26096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pantera<\/a>\n<!-- Time to render name section of link id 26096: 5.9604644775391E-6 --> \n<\/td>\n<td><p class=\"heading-element\" dir=\"auto\">Identification of transposable element families from pangenome polymorphisms. A pangenome is a collection of genomes or haplotypes that can be aligned and stored as a variation graph in gfa format. pantera receives as input a list of gfa files of non overlapping variation graphs and produces a library of transposable elements found to be polymorphic on that pangenome.<\/p>\n<!-- Time to render link large description section of link id 26096: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pantera> How to use <\/a>\n<!-- Time to render notes section of link id 26096: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26096: 0.00048494338989258 --> \n<tr><td><a href=\"https:\/\/pantools.readthedocs.io\/en\/latest\/\" id=\"link-25000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanTools<\/a>\n<!-- Time to render name section of link id 25000: 6.9141387939453E-6 --> \n<\/td>\n<td><p>PanTools is a toolkit for comparative analysis of large number of genomes.<\/p>\n<!-- Time to render link large description section of link id 25000: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanTools> How to use <\/a>\n<!-- Time to render notes section of link id 25000: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25000: 0.00047993659973145 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/paragraph\" id=\"link-24430\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Paragraph<\/a>\n<!-- Time to render name section of link id 24430: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Graph realignment tools for structural variants.<\/p>\n<!-- Time to render link large description section of link id 24430: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Paragraph> How to use <\/a>\n<!-- Time to render notes section of link id 24430: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24430: 0.00046014785766602 --> \n<tr><td><a href=\"https:\/\/www.gnu.org\/software\/parallel\/\" id=\"link-23898\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">parallel<\/a>\n<!-- Time to render name section of link id 23898: 6.9141387939453E-6 --> \n<\/td>\n<td><p>GNU parallel is a shell tool for executing jobs in parallel using one or more computers.<\/p>\n<!-- Time to render link large description section of link id 23898: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> default system\n<!-- Time to render notes section of link id 23898: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23898: 0.00048017501831055 --> \n<tr><td><a href=\"https:\/\/github.com\/rvalieris\/parallel-fastq-dump\" id=\"link-24431\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">parallel-fastq-dump<\/a>\n<!-- Time to render name section of link id 24431: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file (see the protip below). This tool speeds up the process by dividing the work into multiple threads.<\/p>\n<!-- Time to render link large description section of link id 24431: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_parallel-fastq-dump> How to use <\/a>\n<!-- Time to render notes section of link id 24431: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24431: 0.00020003318786621 --> \n<tr><td><a href=\"https:\/\/github.com\/BenoitMorel\/ParGenes\" id=\"link-24432\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ParGenes<\/a>\n<!-- Time to render name section of link id 24432: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A massively parallel tool for model selection and tree inference on thousands of genes.<\/p>\n<!-- Time to render link large description section of link id 24432: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24432: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24432: 0.00020003318786621 --> \n<tr><td><a href=\"https:\/\/github.com\/YannickJadoul\/Parselmouth\" id=\"link-25809\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Parselmouth<\/a>\n<!-- Time to render name section of link id 25809: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Parselmouth aim to provide a complete and Pythonic interface to the internal Praat code.<\/p>\n<!-- Time to render link large description section of link id 25809: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Parselmouth> How to use <\/a>\n<!-- Time to render notes section of link id 25809: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25809: 0.00020694732666016 --> \n<tr><td><a href=\"https:\/\/github.com\/4ureliek\/Parsing-RepeatMasker-Outputs\" id=\"link-24433\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">parseRM<\/a>\n<!-- Time to render name section of link id 24433: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Few scripts facilitating the extraction of info from Repeat Masker .out files<\/p>\n<!-- Time to render link large description section of link id 24433: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24433: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24433: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/parsnp\" id=\"link-24971\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Parsnp<\/a>\n<!-- Time to render name section of link id 24971: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.<\/p>\n<!-- Time to render link large description section of link id 24971: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Parsnp> How to use <\/a>\n<!-- Time to render notes section of link id 24971: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24971: 0.00020194053649902 --> \n<tr><td><a href=\"http:\/\/www.robertlanfear.com\/partitionfinder\/\" id=\"link-23686\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PartitionFinder<\/a>\n<!-- Time to render name section of link id 23686: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.<\/p>\n<!-- Time to render link large description section of link id 23686: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PartitionFinder> How to use <\/a>\n<!-- Time to render notes section of link id 23686: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23686: 0.00020980834960938 --> \n<tr><td><a href=\"https:\/\/github.com\/PASApipeline\/PASApipeline\" id=\"link-23687\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PASApipeline<\/a>\n<!-- Time to render name section of link id 23687: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.<\/p>\n<!-- Time to render link large description section of link id 23687: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PASApipeline> How to use <\/a>\n<!-- Time to render notes section of link id 23687: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23687: 0.0001988410949707 --> \n<tr><td><a href=\"https:\/\/github.com\/smirarab\/pasta\" id=\"link-24116\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PASTA<\/a>\n<!-- Time to render name section of link id 24116: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PASTA estimates alignments and ML trees from unaligned sequences using an iterative approach. In each iteration, it first estimates a multiple sequence alignment using the current tree as a guide and then estimates an ML tree on (a masked version of) the alignment.<\/p>\n<!-- Time to render link large description section of link id 24116: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PASTA> How to use <\/a>\n<!-- Time to render notes section of link id 24116: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24116: 0.0001988410949707 --> \n<tr><td><a href=\"https:\/\/git-r3lab.uni.lu\/laura.denies\/PathoFact\" id=\"link-24434\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PathoFact<\/a>\n<!-- Time to render name section of link id 24434: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance.<\/p>\n<!-- Time to render link large description section of link id 24434: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24434: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24434: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/ruidlpm\/pathPhynder\" id=\"link-25161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pathPhynder<\/a>\n<!-- Time to render name section of link id 25161: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A workflow for integrating ancient lineages into present-day phylogenies.<\/p>\n<!-- Time to render link large description section of link id 25161: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pathPhynder> How to use <\/a>\n<!-- Time to render notes section of link id 25161: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25161: 0.00021195411682129 --> \n<tr><td><a href=\"http:\/\/phylosolutions.com\/paup-test\/\" id=\"link-23873\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PAUP<\/a>\n<!-- Time to render name section of link id 23873: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tools for inferring and interpreting phylogenetic trees<\/p>\n<!-- Time to render link large description section of link id 23873: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PAUP> How to use <\/a>\n<!-- Time to render notes section of link id 23873: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23873: 0.0001988410949707 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbbioconda\" id=\"link-23992\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pb-assembly<\/a>\n<!-- Time to render name section of link id 23992: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PacBio\u00ae tools\u00a0 :\u00a0 everything needed to run Falcon and Unzip<\/p>\n<!-- Time to render link large description section of link id 23992: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23992: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23992: 0.0001990795135498 --> \n<tr><td><a href=\"https:\/\/icebert.github.io\/pblat\/\" id=\"link-24435\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pblat<\/a>\n<!-- Time to render name section of link id 24435: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Parallelized blat with multi-threads support.<\/p>\n<!-- Time to render link large description section of link id 24435: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pblat> How to use <\/a>\n<!-- Time to render notes section of link id 24435: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24435: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbmm2\" id=\"link-25904\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pbmm2<\/a>\n<!-- Time to render name section of link id 25904: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A minimap2 frontend for PacBio native data format.<\/p>\n<!-- Time to render link large description section of link id 25904: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pbmm2> How to use <\/a>\n<!-- Time to render notes section of link id 25904: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25904: 0.00020909309387207 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbtk\" id=\"link-25472\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pbtk<\/a>\n<!-- Time to render name section of link id 25472: 2.1457672119141E-6 --> \n<\/td>\n<td><p dir=\"auto\" style=\"text-align: left\" align=\"center\">PacBio BAM toolkit<\/p>\n<!-- Time to render link large description section of link id 25472: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pbtk> How to use <\/a>\n<!-- Time to render notes section of link id 25472: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25472: 0.00021481513977051 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/pcadmix\/home\" id=\"link-23688\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PCAdmix<\/a>\n<!-- Time to render name section of link id 23688: 2.8610229492188E-6 --> \n<\/td>\n<td><p><span style=\"font-family: Helvetica\">PCAdmix is a method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes.\u00a0 The method considers data chromosome by chromosome.<\/span><\/p>\n<!-- Time to render link large description section of link id 23688: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23688: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23688: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/Rosemeis\/pcangsd\" id=\"link-24019\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PCAngsd<\/a>\n<!-- Time to render name section of link id 24019: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Framework for analyzing low depth next-generation sequencing (NGS) data in heterogeneous populations using principal component analysis (PCA).<\/p>\n<!-- Time to render link large description section of link id 24019: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PCAngsd> How to use <\/a>\n<!-- Time to render notes section of link id 24019: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24019: 0.00017690658569336 --> \n<tr><td><a href=\"http:\/\/sco.h-its.org\/exelixis\/web\/software\/pear\/index.html\" id=\"link-23783\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PEAR<\/a>\n<!-- Time to render name section of link id 23783: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.<\/p>\n<!-- Time to render link large description section of link id 23783: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PEAR> How to use <\/a>\n<!-- Time to render notes section of link id 23783: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23783: 0.00016593933105469 --> \n<tr><td><a href=\"https:\/\/github.com\/lemene\/PECAT\" id=\"link-25450\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PECAT<\/a>\n<!-- Time to render name section of link id 25450: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PECAT is a phased error correction and assembly tool for long reads. It includes a haplotype-aware correction method and an efficient diploid assembly method.<\/p>\n<!-- Time to render link large description section of link id 25450: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PECAT> How to use <\/a>\n<!-- Time to render notes section of link id 25450: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25450: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/gitlab.in2p3.fr\/phoogle\/pelican\" id=\"link-25083\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pelican<\/a>\n<!-- Time to render name section of link id 25083: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pelican is a reimplementation of the model of Tamuri et al. (2009) to identify sites undergoing different kinds of directional selection in different parts of a phylogenetic tree.<\/p>\n<!-- Time to render link large description section of link id 25083: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pelican> How to use <\/a>\n<!-- Time to render notes section of link id 25083: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25083: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/cschin\/peregrine-2021\" id=\"link-24093\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Peregrine<\/a>\n<!-- Time to render name section of link id 24093: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Peregrine is a fast genome assembler for accurate long reads (length &gt; 10kb, accuraccy &gt; 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus.<\/p>\n<!-- Time to render link large description section of link id 24093: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Peregrine> How to use <\/a>\n<!-- Time to render notes section of link id 24093: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24093: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/rth.dk\/resources\/petfold\/\" id=\"link-24436\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PETfold<\/a>\n<!-- Time to render name section of link id 24436: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PETfold performs Probabilistic Evolutionary and Thermodynamic folding of a multiple alignment of RNA sequences.<\/p>\n<!-- Time to render link large description section of link id 24436: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24436: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24436: 0.00018191337585449 --> \n<tr><td><a href=\"ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/Pfam\/Tools\/\" id=\"link-24437\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PfamScan<\/a>\n<!-- Time to render name section of link id 24437: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A program that searches a FASTA file against a library of Pfam HMMs.<\/p>\n<!-- Time to render link large description section of link id 24437: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PfamScan> How to use <\/a>\n<!-- Time to render notes section of link id 24437: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24437: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/sib-swiss\/pftools3\" id=\"link-23689\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pftools3<\/a>\n<!-- Time to render name section of link id 23689: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases<\/p>\n<!-- Time to render link large description section of link id 23689: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pftools3> How to use <\/a>\n<!-- Time to render notes section of link id 23689: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23689: 0.0001680850982666 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/pgap\" id=\"link-24438\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PGAP<\/a>\n<!-- Time to render name section of link id 24438: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).<\/p>\n<!-- Time to render link large description section of link id 24438: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pgap> How to use <\/a>\n<!-- Time to render notes section of link id 24438: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24438: 0.00018596649169922 --> \n<tr><td><a href=\"http:\/\/www.cmpg.unibe.ch\/software\/PGDSpider\/\" id=\"link-23690\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PGDSpider<\/a>\n<!-- Time to render name section of link id 23690: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances)<\/p>\n<!-- Time to render link large description section of link id 23690: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PGDSpider> How to use <\/a>\n<!-- Time to render notes section of link id 23690: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23690: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/pangenome\/pggb\" id=\"link-24887\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pggb<\/a>\n<!-- Time to render name section of link id 24887: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Pangenome graph builder.<\/p>\n<!-- Time to render link large description section of link id 24887: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pggb> How to use <\/a>\n<!-- Time to render notes section of link id 24887: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24887: 0.00019288063049316 --> \n<tr><td><a href=\"http:\/\/www.bioinf.man.ac.uk\/resources\/phase\/\" id=\"link-23772\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHASE<\/a>\n<!-- Time to render name section of link id 23772: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PHASE is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.<\/p>\n<!-- Time to render link large description section of link id 23772: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHASE> How to use <\/a>\n<!-- Time to render notes section of link id 23772: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23772: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/github.com\/phasebook\/phasebook\" id=\"link-24439\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phasebook<\/a>\n<!-- Time to render name section of link id 24439: 2.8610229492188E-6 --> \n<\/td>\n<td><p>phasebook is a novel approach for reconstructing the haplotypes of diploid genomes from long reads de novo, that is without the need for a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24439: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24439: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24439: 0.0001671314239502 --> \n<tr><td><a href=\"http:\/\/phasetank.sourceforge.net\" id=\"link-24440\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhaseTank<\/a>\n<!-- Time to render name section of link id 24440: 2.8610229492188E-6 --> \n<\/td>\n<td><p>To systemically characterize phasiRNAs\/tasiRNAs and their regulatory cascades 'miRNA\/phasiRNA -&amp;gt<\/p>\n<!-- Time to render link large description section of link id 24440: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24440: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24440: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/compgen.cshl.edu\/phast\/\" id=\"link-24866\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHAST<\/a>\n<!-- Time to render name section of link id 24866: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Phylogenetic Analysis with Space\/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics.<\/p>\n<!-- Time to render link large description section of link id 24866: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHAST> How to use <\/a>\n<!-- Time to render notes section of link id 24866: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24866: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/boulund\/phaster_scripts\" id=\"link-25290\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHASTER_scripts<\/a>\n<!-- Time to render name section of link id 25290: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Small utility scripts to query the PHASTER API endpoint, to identify and annotate prophage sequences within bacterial genomes and plasmids.<\/p>\n<!-- Time to render link large description section of link id 25290: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHASTER_scripts> How to use <\/a>\n<!-- Time to render notes section of link id 25290: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25290: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/www.maths.otago.ac.nz\/~dbryant\/software\/phimanual.pdf\" id=\"link-23864\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhiPack<\/a>\n<!-- Time to render name section of link id 23864: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The Phi Test is a simple, rapid, and statistically efficient test for recombination.<\/p>\n<!-- Time to render link large description section of link id 23864: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23864: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23864: 0.0001680850982666 --> \n<tr><td><a href=\"https:\/\/github.com\/linsalrob\/PhiSpy\" id=\"link-24441\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhiSpy<\/a>\n<!-- Time to render name section of link id 24441: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.<\/p>\n<!-- Time to render link large description section of link id 24441: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24441: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24441: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/phobius.sbc.su.se\/index.html\" id=\"link-23956\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Phobius<\/a>\n<!-- Time to render name section of link id 23956: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A combined transmembrane topology and signal peptide predictor.<\/p>\n<!-- Time to render link large description section of link id 23956: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23956: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23956: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/MEEIBioinformaticsCenter\/phy-mer\" id=\"link-24442\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Phy-Mer<\/a>\n<!-- Time to render name section of link id 24442: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A novel alignment-free and reference-independent mitochondrial haplogroup classifier.<\/p>\n<!-- Time to render link large description section of link id 24442: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24442: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24442: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/JLSteenwyk\/PhyKIT\" id=\"link-24443\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyKIT<\/a>\n<!-- Time to render name section of link id 24443: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.<\/p>\n<!-- Time to render link large description section of link id 24443: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyKIT> How to use <\/a>\n<!-- Time to render notes section of link id 24443: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24443: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/evolution.genetics.washington.edu\/phylip.html\" id=\"link-23691\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHYLIP<\/a>\n<!-- Time to render name section of link id 23691: 3.0994415283203E-6 --> \n<\/td>\n<td><div>PHYLIP (PHYLogeny Inference Package), is a package composed by 34 programs dedicated to phylogeny inference. Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.<\/div>\n<!-- Time to render link large description section of link id 23691: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHYLIP> How to use <\/a>\n<!-- Time to render notes section of link id 23691: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23691: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/megasun.bch.umontreal.ca\/People\/lartillot\/www\/download.html\" id=\"link-23692\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyloBayes<\/a>\n<!-- Time to render name section of link id 23692: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction and molecular dating using protein and nucleic acid alignments.<\/p>\n<!-- Time to render link large description section of link id 23692: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyloBayes> How to use <\/a>\n<!-- Time to render notes section of link id 23692: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23692: 0.00017786026000977 --> \n<tr><td><a href=\"http:\/\/megasun.bch.umontreal.ca\/People\/lartillot\/www\/downloadmpi.html\" id=\"link-23872\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Phylobayes_MPI<\/a>\n<!-- Time to render name section of link id 23872: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PhyloBayes (Lartillot et al, 2009) is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. With MPI.<\/p>\n<!-- Time to render link large description section of link id 23872: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyloBayes_MPI> How to use <\/a>\n<!-- Time to render notes section of link id 23872: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23872: 0.00016307830810547 --> \n<tr><td><a href=\"http:\/\/hrgv.github.io\/phyloFlash\" id=\"link-25094\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phyloFlash<\/a>\n<!-- Time to render name section of link id 25094: 1.0013580322266E-5 --> \n<\/td>\n<td><p>phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.<\/p>\n<!-- Time to render link large description section of link id 25094: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_phyloFlash> How to use <\/a>\n<!-- Time to render notes section of link id 25094: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25094: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/bioinfocs.rice.edu\/phylonet\" id=\"link-24444\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyloNet<\/a>\n<!-- Time to render name section of link id 24444: 2.1457672119141E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 24444: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyloNet> How to use <\/a>\n<!-- Time to render notes section of link id 24444: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24444: 0.00027680397033691 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/nsegata\/phylophlan\/wiki\/Home\" id=\"link-24062\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyloPhlAn<\/a>\n<!-- Time to render name section of link id 24062: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. The pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations.<\/p>\n<!-- Time to render link large description section of link id 24062: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24062: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24062: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/phyluce.readthedocs.io\" id=\"link-24445\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phyluce<\/a>\n<!-- Time to render name section of link id 24445: 1.9073486328125E-6 --> \n<\/td>\n<td><p>phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.<\/p>\n<!-- Time to render link large description section of link id 24445: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_phyluce> How to use <\/a>\n<!-- Time to render notes section of link id 24445: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24445: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/stephaneguindon\/phyml\" id=\"link-23693\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyML<\/a>\n<!-- Time to render name section of link id 23693: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PhyML is a phylogeny software based on the maximum-likelihood principle.<\/p>\n<!-- Time to render link large description section of link id 23693: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyML> How to use <\/a>\n<!-- Time to render notes section of link id 23693: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23693: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/FePhyFoFum\/phyx\" id=\"link-23957\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phyx<\/a>\n<!-- Time to render name section of link id 23957: 3.0994415283203E-6 --> \n<\/td>\n<td><p>phyx performs phylogenetics analyses on trees and sequences.<\/p>\n<!-- Time to render link large description section of link id 23957: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23957: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23957: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/broadinstitute.github.io\/picard\/\" id=\"link-23694\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">picard-tools<\/a>\n<!-- Time to render name section of link id 23694: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.<\/p>\n<!-- Time to render link large description section of link id 23694: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_picard-tools> How to use <\/a>\n<!-- Time to render notes section of link id 23694: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23694: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/picrust\/picrust2\" id=\"link-23695\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PICRUSt<\/a>\n<!-- Time to render name section of link id 23695: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PICRUSt (pronounced \uff93pie crust\uff94) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.<\/p>\n<!-- Time to render link large description section of link id 23695: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PICRUSt2> How to use <\/a>\n<!-- Time to render notes section of link id 23695: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23695: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/www.drive5.com\/piler\/\" id=\"link-24446\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PILER<\/a>\n<!-- Time to render name section of link id 24446: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Genomic repeat analysis software.<\/p>\n<!-- Time to render link large description section of link id 24446: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PILER> How to use <\/a>\n<!-- Time to render notes section of link id 24446: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24446: 0.00016403198242188 --> \n<tr><td><a href=\"http:\/\/www.drive5.com\/pilercr\/\" id=\"link-24447\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PILERCR<\/a>\n<!-- Time to render name section of link id 24447: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PILERCR is public domain software for finding CRISPR repeats.<\/p>\n<!-- Time to render link large description section of link id 24447: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24447: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24447: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/broadinstitute\/pilon\" id=\"link-23821\" class=\"track_this_link \" rel=\"noopener noreferrer\">Pilon<\/a>\n<!-- Time to render name section of link id 23821: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pilon is an automated genome assembly improvement and variant detection tool.<\/p>\n<!-- Time to render link large description section of link id 23821: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pilon> How to use <\/a>\n<!-- Time to render notes section of link id 23821: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23821: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/www.haplotype.org\/software.html\" id=\"link-24448\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">piMASS<\/a>\n<!-- Time to render name section of link id 24448: 1.9073486328125E-6 --> \n<\/td>\n<td><p>posterior inference via Model Averaging and Subset Selection: performs genome-wide joint analysis of all SNPs in association with a phenotype.<\/p>\n<!-- Time to render link large description section of link id 24448: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24448: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24448: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/gmt.genome.wustl.edu\/packages\/pindel\/index.html\" id=\"link-23696\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pindel<\/a>\n<!-- Time to render name section of link id 23696: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.<\/p>\n<!-- Time to render link large description section of link id 23696: 0.00023794174194336 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pindel> How to use <\/a>\n<!-- Time to render notes section of link id 23696: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23696: 0.00042605400085449 --> \n<tr><td><a href=\"https:\/\/github.com\/suhrig\/pingpongpro\" id=\"link-24449\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PingPongPro<\/a>\n<!-- Time to render name section of link id 24449: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Find ping-pong signatures in piRNA-Seq data like a pro.<\/p>\n<!-- Time to render link large description section of link id 24449: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24449: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24449: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/pixy.readthedocs.io\/en\/latest\/about.html\" id=\"link-25559\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pixy<\/a>\n<!-- Time to render name section of link id 25559: 3.0994415283203E-6 --> \n<\/td>\n<td>pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (\u03c0) and between (dxy) populations from a VCF.\n<!-- Time to render link large description section of link id 25559: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pixy> How to use <\/a>\n<!-- Time to render notes section of link id 25559: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25559: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/pmelsted\/pizzly\" id=\"link-24450\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pizzly<\/a>\n<!-- Time to render name section of link id 24450: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A program for detecting gene fusions from RNA-Seq data of cancer samples.<\/p>\n<!-- Time to render link large description section of link id 24450: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24450: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24450: 0.00018811225891113 --> \n<tr><td><a href=\"https:\/\/github.com\/plantismash\/plantismash\" id=\"link-25929\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlantiSMASH<\/a>\n<!-- Time to render name section of link id 25929: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PlantiSMASH is a specialized extension of antiSMASH for the identification and analysis of biosynthetic gene clusters (BGCs) in plant genomes. It supports advanced plant-specific detection rules and features for comparative genomics, visualization, and more.<\/p>\n<!-- Time to render link large description section of link id 25929: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlantiSMASH> How to use <\/a>\n<!-- Time to render notes section of link id 25929: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25929: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/smaegol\/PlasFlow\" id=\"link-24776\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlasFlow<\/a>\n<!-- Time to render name section of link id 24776: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software for prediction of plasmid sequences in metagenomic assemblies.<\/p>\n<!-- Time to render link large description section of link id 24776: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlasFlow> How to use <\/a>\n<!-- Time to render notes section of link id 24776: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24776: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/nekokoe\/Plasmer\" id=\"link-25217\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Plasmer<\/a>\n<!-- Time to render name section of link id 25217: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.<\/p>\n<!-- Time to render link large description section of link id 25217: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Plasmer> How to use <\/a>\n<!-- Time to render notes section of link id 25217: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25217: 0.0001978874206543 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/plasmidfinder\" id=\"link-24452\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlasmidFinder<\/a>\n<!-- Time to render name section of link id 24452: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The service identifies plasmids in total or partial sequenced isolates of bacteria.<\/p>\n<!-- Time to render link large description section of link id 24452: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlasmidFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24452: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24452: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/plass\" id=\"link-24703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Plass<\/a>\n<!-- Time to render name section of link id 24703: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.<\/p>\n<!-- Time to render link large description section of link id 24703: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24703: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24703: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/gbouras13\/plassembler\" id=\"link-25474\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">plassembler<\/a>\n<!-- Time to render name section of link id 25474: 2.8610229492188E-6 --> \n<\/td>\n<td><p>plassembler is a program that is designed for automated &amp; fast assembly of plasmids in bacterial genomes that have been hybrid sequenced with long read &amp; paired-end short read sequencing.<\/p>\n<!-- Time to render link large description section of link id 25474: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_plassembler> How to use <\/a>\n<!-- Time to render notes section of link id 25474: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25474: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/plast.inria.fr\" id=\"link-23697\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PLAST<\/a>\n<!-- Time to render name section of link id 23697: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.<\/p>\n<!-- Time to render link large description section of link id 23697: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23697: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23697: 0.00018000602722168 --> \n<tr><td><a href=\"http:\/\/platanus.bio.titech.ac.jp\/platanus-assembler\" id=\"link-24453\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Platanus<\/a>\n<!-- Time to render name section of link id 24453: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24453: 0.00049805641174316 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24453: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24453: 0.00068092346191406 --> \n<tr><td><a href=\"http:\/\/platanus.bio.titech.ac.jp\/pltanus_trim\" id=\"link-24454\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Platanus_trim<\/a>\n<!-- Time to render name section of link id 24454: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Platanus_trim is a tool for trimming adaptor sequences and low quality regions. In contrast, Platanus_internal_trim is a tool for trimming internal adaptor sequence, adaptor sequences, and low quality regions. Platanus_trim is designed for paired-end library and Platanus_internal_trim is for mate-pair library.<\/p>\n<!-- Time to render link large description section of link id 24454: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24454: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24454: 0.0001671314239502 --> \n<tr><td><a href=\"http:\/\/platanus.bio.titech.ac.jp\/platanus2\" id=\"link-24455\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Platanus2<\/a>\n<!-- Time to render name section of link id 24455: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Platanus-allee (Platanus2) is a de novo haplotype assembler (phasing tool), which assembles each haplotype sequence in a diploid genome.<\/p>\n<!-- Time to render link large description section of link id 24455: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24455: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24455: 0.0001990795135498 --> \n<tr><td><a href=\"https:\/\/www.cog-genomics.org\/plink\/\" id=\"link-23698\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PLINK<\/a>\n<!-- Time to render name section of link id 23698: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.<\/p>\n<!-- Time to render link large description section of link id 23698: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PLINK> How to use <\/a>\n<!-- Time to render notes section of link id 23698: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23698: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/diriano\/ploidyNGS\" id=\"link-24081\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ploidyNGS<\/a>\n<!-- Time to render name section of link id 24081: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data.<\/p>\n<!-- Time to render link large description section of link id 24081: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24081: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24081: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/schneebergerlab\/plotsr\" id=\"link-24456\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">plotsr<\/a>\n<!-- Time to render name section of link id 24456: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Tool to plot synteny and structural rearrangements between genomes.<\/p>\n<!-- Time to render link large description section of link id 24456: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_plotsr> How to use <\/a>\n<!-- Time to render notes section of link id 24456: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24456: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/beiko-lab\/PMERGE\" id=\"link-23993\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PMERGE<\/a>\n<!-- Time to render name section of link id 23993: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PMERGE, is a software, which implements a new method that identifies candidate PSVs by building networks of loci that share high levels of nucleotide similarity. The PMERGE is embedded in the analysis pipeline of the widely used Stacks software, and it is straightforward to apply it as an additional filter in population-genomic studies using RAD-seq data.<\/p>\n<!-- Time to render link large description section of link id 23993: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23993: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23993: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/pod5-file-format\" id=\"link-25791\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">POD5<\/a>\n<!-- Time to render name section of link id 25791: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The pod5 Python package contains the tools and python API wrapping the compiled bindings for the POD5 file format from lib_pod5.<\/p>\n<!-- Time to render link large description section of link id 25791: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_POD5> How to use <\/a>\n<!-- Time to render notes section of link id 25791: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25791: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Polypolish\" id=\"link-24457\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Polypolish<\/a>\n<!-- Time to render name section of link id 24457: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Polypolish is a tool for polishing genome assemblies with short reads.<\/p>\n<!-- Time to render link large description section of link id 24457: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Polypolish> How to use <\/a>\n<!-- Time to render notes section of link id 24457: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24457: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/nanoporetech.github.io\/pomoxis\/index.html\" id=\"link-24458\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pomoxis<\/a>\n<!-- Time to render name section of link id 24458: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing.<\/p>\n<!-- Time to render link large description section of link id 24458: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24458: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24458: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/brown.edu\/Research\/Ramachandran_Lab\/projects\/\" id=\"link-23983\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pong<\/a>\n<!-- Time to render name section of link id 23983: 2.8610229492188E-6 --> \n<\/td>\n<td><p>pong is a freely available software package, released by Behr et al. (2016, Bioinformatics), for post-processing output from clustering inference using population genetic data.<\/p>\n<!-- Time to render link large description section of link id 23983: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23983: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23983: 0.0001988410949707 --> \n<tr><td><a href=\"https:\/\/popart.maths.otago.ac.nz\/\" id=\"link-25731\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PopART<\/a>\n<!-- Time to render name section of link id 25731: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PopART (Population Analysis with Reticulate Trees) is free, open source population genetics software that was developed as part of the Allan Wilson Centre Imaging Evolution Initiative.<\/p>\n<!-- Time to render link large description section of link id 25731: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PopART> How to use <\/a>\n<!-- Time to render notes section of link id 25731: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25731: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/bkehr\/popins\" id=\"link-23849\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">popins<\/a>\n<!-- Time to render name section of link id 23849: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Population-scale detection of novel-sequence insertions.<\/p>\n<!-- Time to render link large description section of link id 23849: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23849: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23849: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/kehrlab\/PopIns2\" id=\"link-24998\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PopIns2<\/a>\n<!-- Time to render name section of link id 24998: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs.<\/p>\n<!-- Time to render link large description section of link id 24998: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24998: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24998: 0.00020384788513184 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/popoolation\/?source=navbar\" id=\"link-25272\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PoPoolation<\/a>\n<!-- Time to render name section of link id 25272: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima\u2019s Pi, Watterson\u2019s Theta and Tajima\u2019s D with a sliding window approach for chromosomes or for set of genes.<\/p>\n<!-- Time to render link large description section of link id 25272: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PoPoolation> How to use <\/a>\n<!-- Time to render notes section of link id 25272: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25272: 0.0001990795135498 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/popoolation2\/\" id=\"link-23930\" class=\"track_this_link \" rel=\"noopener noreferrer\">PoPoolation2<\/a>\n<!-- Time to render name section of link id 23930: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution.<\/p>\n<!-- Time to render link large description section of link id 23930: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PoPoolation2> How to use <\/a>\n<!-- Time to render notes section of link id 23930: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23930: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenomics\/popPhylABC\" id=\"link-24459\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">popPhylABC<\/a>\n<!-- Time to render name section of link id 24459: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Scripts used for ABC analysis with homo- and heterogeneity in Migration rates or\/and Effective population sizes<\/p>\n<!-- Time to render link large description section of link id 24459: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24459: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24459: 0.00019693374633789 --> \n<tr><td><a href=\"http:\/\/membres-timc.imag.fr\/Olivier.Francois\/pops.html\" id=\"link-25589\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">POPS<\/a>\n<!-- Time to render name section of link id 25589: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The POPS program performs inference of ancestry distribution models.<\/p>\n<!-- Time to render link large description section of link id 25589: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_POPS> How to use <\/a>\n<!-- Time to render notes section of link id 25589: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25589: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Porechop#requirements\" id=\"link-23850\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Porechop<\/a>\n<!-- Time to render name section of link id 23850: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.<\/p>\n<!-- Time to render link large description section of link id 23850: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Porechop> How to use <\/a>\n<!-- Time to render notes section of link id 23850: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23850: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/bonsai-team\/Porechop_ABI\" id=\"link-24099\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Porechop_ABI<\/a>\n<!-- Time to render name section of link id 24099: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Porechop_abi (ab initio) is an extension of Porechop that is able to infer the adapter sequence from the Oxford Nanopore reads. It discovers the adapter sequence from the reads using approximate k-mers and assembly, and add the sequence found to the adapter list (adapters.py file).<\/p>\n<!-- Time to render link large description section of link id 24099: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Porechop_ABI> How to use <\/a>\n<!-- Time to render notes section of link id 24099: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24099: 0.00019383430480957 --> \n<tr><td><a href=\"https:\/\/portcullis.readthedocs.io\/en\/latest\/\" id=\"link-23986\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Portcullis<\/a>\n<!-- Time to render name section of link id 23986: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Splice junction analysis and filtering from BAM files.<\/p>\n<!-- Time to render link large description section of link id 23986: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23986: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23986: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/packages.debian.org\/jessie\/pp-popularity-contest\" id=\"link-24067\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pp-popularity-contest<\/a>\n<!-- Time to render name section of link id 24067: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The pp-popularity-contest package sets up a cron job that periodically submits the developers anonymous statistics on the usage of Rost Lab prediction methods installed on this system.<\/p>\n<!-- Time to render link large description section of link id 24067: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pp-popularity-contest> How to use <\/a>\n<!-- Time to render notes section of link id 24067: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24067: 0.0001671314239502 --> \n<tr><td><a href=\"https:\/\/github.com\/labgem\/PPanGGOLiN\" id=\"link-25706\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PPanGGOLiN<\/a>\n<!-- Time to render name section of link id 25706: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations.<\/p>\n<!-- Time to render link large description section of link id 25706: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PPanGGOLiN> How to use <\/a>\n<!-- Time to render notes section of link id 25706: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25706: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/ariloytynoja.github.io\/prank-msa\/\" id=\"link-24048\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PRANK<\/a>\n<!-- Time to render name section of link id 24048: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.<\/p>\n<!-- Time to render link large description section of link id 24048: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PRANK> How to use <\/a>\n<!-- Time to render notes section of link id 24048: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24048: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/BolognaBiocomp\/predgpi\" id=\"link-25470\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PredGPI<\/a>\n<!-- Time to render name section of link id 25470: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Prediction of glycosylphosphatidylinositol-anchors in proteins based on HMMs and SVMs.<\/p>\n<!-- Time to render link large description section of link id 25470: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PredGPI> How to use <\/a>\n<!-- Time to render notes section of link id 25470: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25470: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/bmda.dmi.unibas.ch\/software.html\" id=\"link-24460\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PredictHaplo<\/a>\n<!-- Time to render name section of link id 24460: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This software aims at reconstructing haplotypes from next-generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24460: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PredictHaplo> How to use <\/a>\n<!-- Time to render notes section of link id 24460: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24460: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/smithlabcode\/preseq\" id=\"link-24461\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">preseq<\/a>\n<!-- Time to render name section of link id 24461: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software for predicting library complexity and genome coverage in high-throughput sequencing.<\/p>\n<!-- Time to render link large description section of link id 24461: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_preseq> How to use <\/a>\n<!-- Time to render notes section of link id 24461: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24461: 0.00019598007202148 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-tol\/PretextMap\" id=\"link-25528\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PretextMap<\/a>\n<!-- Time to render name section of link id 25528: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps. Full suite of Pretext tools.<\/p>\n<!-- Time to render link large description section of link id 25528: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PretextMap> How to use <\/a>\n<!-- Time to render notes section of link id 25528: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25528: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-tol\/PretextView\" id=\"link-25527\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PretextView<\/a>\n<!-- Time to render name section of link id 25527: 3.0994415283203E-6 --> \n<\/td>\n<td><p>OpenGL Powered Pretext Contact Map Viewer.<\/p>\n<!-- Time to render link large description section of link id 25527: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PretextView> How to use <\/a>\n<!-- Time to render notes section of link id 25527: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25527: 0.00022196769714355 --> \n<tr><td><a href=\"http:\/\/primer3.org\/\" id=\"link-23699\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Primer3<\/a>\n<!-- Time to render name section of link id 23699: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Primer3 is a widely used program for designing PCR primers (PCR = \"Polymerase Chain Reaction\").<\/p>\n<!-- Time to render link large description section of link id 23699: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Primer3> How to use <\/a>\n<!-- Time to render notes section of link id 23699: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23699: 0.00019311904907227 --> \n<tr><td><a href=\"http:\/\/prinseq.sourceforge.net\" id=\"link-24027\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PRINSEQ<\/a>\n<!-- Time to render name section of link id 24027: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.<\/p>\n<!-- Time to render link large description section of link id 24027: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PRINSEQ> How to use <\/a>\n<!-- Time to render notes section of link id 24027: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24027: 0.00042200088500977 --> \n<tr><td><a href=\"http:\/\/probcons.stanford.edu\/about.html\" id=\"link-24462\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROBCONSRNA<\/a>\n<!-- Time to render name section of link id 24462: 6.9141387939453E-6 --> \n<\/td>\n<td><p>PROBCONS is a tool for generating multiple alignments of protein sequences.<\/p>\n<!-- Time to render link large description section of link id 24462: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24462: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24462: 0.00053310394287109 --> \n<tr><td><a href=\"http:\/\/prodigal.ornl.gov\/\" id=\"link-23700\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Prodigal<\/a>\n<!-- Time to render name section of link id 23700: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Prodigal (<b>Pro<\/b>karyotic <b>Dy<\/b>namic Programming <b>G<\/b>enefinding <b>Al<\/b>gorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.<\/p>\n<!-- Time to render link large description section of link id 23700: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Prodigal> How to use <\/a>\n<!-- Time to render notes section of link id 23700: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23700: 0.0005791187286377 --> \n<tr><td><a href=\"https:\/\/github.com\/glennhickey\/progressiveCactus\" id=\"link-23953\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProgressiveCactus<\/a>\n<!-- Time to render name section of link id 23953: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Progressive Cactus is a whole-genome alignment package.<\/p>\n<!-- Time to render link large description section of link id 23953: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23953: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23953: 0.00050115585327148 --> \n<tr><td><a href=\"https:\/\/github.com\/OSGeo\/proj.4\" id=\"link-23790\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROJ4<\/a>\n<!-- Time to render name section of link id 23790: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Cartographic Projections Library<\/p>\n<!-- Time to render link large description section of link id 23790: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23790: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23790: 0.00050091743469238 --> \n<tr><td><a href=\"https:\/\/github.com\/tseemann\/prokka\" id=\"link-23701\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROKKA<\/a>\n<!-- Time to render name section of link id 23701: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank\/DDJB\/ENA.<\/p>\n<!-- Time to render link large description section of link id 23701: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PROKKA> How to use <\/a>\n<!-- Time to render notes section of link id 23701: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23701: 0.00031614303588867 --> \n<tr><td><a href=\"https:\/\/github.com\/BioinformaticsLabAtMUN\/PromoTech\" id=\"link-25544\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PromoTech<\/a>\n<!-- Time to render name section of link id 25544: 3.814697265625E-6 --> \n<\/td>\n<td>Promotech is a machine-learning-based classifier trained to generate a model that generalizes and detects promoters in a wide range of bacterial species.\n<!-- Time to render link large description section of link id 25544: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Promotech> How to use <\/a>\n<!-- Time to render notes section of link id 25544: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25544: 0.00031805038452148 --> \n<tr><td><a href=\"https:\/\/github.com\/jaumlrc\/ProphET\" id=\"link-24463\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProphET<\/a>\n<!-- Time to render name section of link id 24463: 4.0531158447266E-6 --> \n<\/td>\n<td><p>ProphET, Prophage Estimation Tool: a standalone prophage sequence prediction tool with self-updating reference database.<\/p>\n<!-- Time to render link large description section of link id 24463: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24463: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24463: 0.00030088424682617 --> \n<tr><td><a href=\"https:\/\/prost.readthedocs.io\" id=\"link-25118\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Prost<\/a>\n<!-- Time to render name section of link id 25118: 4.0531158447266E-6 --> \n<\/td>\n<td><p><em>Prost!<\/em>\u00a0(PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform.\u00a0<em>Prost!<\/em>\u00a0does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single\u00a0<em>Prost!<\/em>\u00a0run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location,\u00a0<em>Prost!<\/em>\u00a0then annotates them using a user-defined annotation database (public or personal annotation database).<\/p>\n<!-- Time to render link large description section of link id 25118: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Prost> How to use <\/a>\n<!-- Time to render notes section of link id 25118: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25118: 0.00030303001403809 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/paulklemm_PHD\/proteinortho\" id=\"link-25229\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Proteinortho<\/a>\n<!-- Time to render name section of link id 25229: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Proteinortho is a tool to detect orthologous genes within different species.<\/p>\n<!-- Time to render link large description section of link id 25229: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Proteinortho> How to use <\/a>\n<!-- Time to render notes section of link id 25229: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25229: 0.00030112266540527 --> \n<tr><td><a href=\"https:\/\/github.com\/isabelschober\/proteinortho_curves\" id=\"link-25230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">proteinortho_curves<\/a>\n<!-- Time to render name section of link id 25230: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Draw pan- and core-genome curves from proteinortho output<\/p>\n<!-- Time to render link large description section of link id 25230: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_proteinortho_curves> How to use <\/a>\n<!-- Time to render notes section of link id 25230: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25230: 0.00031399726867676 --> \n<tr><td><a href=\"https:\/\/github.com\/gatech-genemark\/ProtHint\" id=\"link-24464\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProtHint<\/a>\n<!-- Time to render name section of link id 24464: 4.0531158447266E-6 --> \n<\/td>\n<td><p>ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.<\/p>\n<!-- Time to render link large description section of link id 24464: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ProtHint> How to use <\/a>\n<!-- Time to render notes section of link id 24464: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24464: 0.00030303001403809 --> \n<tr><td><a href=\"https:\/\/github.com\/agemagician\/ProtTrans\" id=\"link-26207\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProtTrans<\/a>\n<!-- Time to render name section of link id 26207: 4.0531158447266E-6 --> \n<\/td>\n<td><p>ProtTrans is providing state of the art pretrained language models for proteins.<\/p>\n<!-- Time to render link large description section of link id 26207: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ProtTrans> How to use <\/a>\n<!-- Time to render notes section of link id 26207: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26207: 0.0003049373626709 --> \n<tr><td><a href=\"http:\/\/provean.jcvi.org\" id=\"link-24465\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROVEAN<\/a>\n<!-- Time to render name section of link id 24465: 4.0531158447266E-6 --> \n<\/td>\n<td><p>PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.<\/p>\n<!-- Time to render link large description section of link id 24465: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PROVEAN> How to use <\/a>\n<!-- Time to render notes section of link id 24465: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24465: 0.00030183792114258 --> \n<tr><td><a href=\"https:\/\/github.com\/salzberg-lab\/PSAURON\" id=\"link-25414\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PSAURON<\/a>\n<!-- Time to render name section of link id 25414: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PSAURON is a machine learning model for rapid assessment of protein coding gene annotation.<\/p>\n<!-- Time to render link large description section of link id 25414: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PSAURON> How to use <\/a>\n<!-- Time to render notes section of link id 25414: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25414: 0.00020909309387207 --> \n<tr><td><a href=\"https:\/\/github.com\/filip-husnik\/pseudofinder\" id=\"link-25019\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pseudofinder<\/a>\n<!-- Time to render name section of link id 25019: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Detection of pseudogene candidates in bacterial and archaeal genomes.<\/p>\n<!-- Time to render link large description section of link id 25019: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 25019: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25019: 0.00019288063049316 --> \n<tr><td><a href=\"http:\/\/deweylab.biostat.wisc.edu\/psginfer\/\" id=\"link-24466\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PSGInfer<\/a>\n<!-- Time to render name section of link id 24466: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PSGInfer is a software package for the analysis of RNA-Seq data with probabilistic splice graph (PSG) models of gene alternative processing (splicing, transcription initiation, and polyadenylation)<\/p>\n<!-- Time to render link large description section of link id 24466: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24466: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24466: 0.00028514862060547 --> \n<tr><td><a href=\"https:\/\/github.com\/wososa\/PSI-Sigma\" id=\"link-24467\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PSI-Sigma<\/a>\n<!-- Time to render name section of link id 24467: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. However, previous PSI-detection methods are limited to specific types of AS events. PSI-Sigma is using a new splicing index (PSI\u03a3) that is more flexible, can incoporate novel junctions, and can compute PSI values of individual exons in complex splicing events.<\/p>\n<!-- Time to render link large description section of link id 24467: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24467: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24467: 0.00031208992004395 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/psmc\" id=\"link-23856\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">psmc<\/a>\n<!-- Time to render name section of link id 23856: 3.814697265625E-6 --> \n<\/td>\n<td><p>This software package infers population size history from a diploid sequence<br \/>\r\nusing the Pairwise Sequentially Markovian Coalescent (PSMC) model.<\/p>\n<!-- Time to render link large description section of link id 23856: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_psmc> How to use <\/a>\n<!-- Time to render notes section of link id 23856: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23856: 0.00027704238891602 --> \n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/pufferfish\" id=\"link-24468\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Puffaligner<\/a>\n<!-- Time to render name section of link id 24468: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Puffaligner is a fast, sensitive and accurate aligner built on top of the Pufferfish index.<\/p>\n<!-- Time to render link large description section of link id 24468: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24468: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24468: 0.00027704238891602 --> \n<tr><td><a href=\"https:\/\/github.com\/dfguan\/purge_dups\" id=\"link-24469\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Purge_Dups<\/a>\n<!-- Time to render name section of link id 24469: 3.814697265625E-6 --> \n<\/td>\n<td><p>purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.<\/p>\n<!-- Time to render link large description section of link id 24469: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Purge_Dups> How to use <\/a>\n<!-- Time to render notes section of link id 24469: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24469: 0.00027799606323242 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/mroachawri\/purge_haplotigs\" id=\"link-24051\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Purge_Haplotigs<\/a>\n<!-- Time to render name section of link id 24051: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Pipeline to help with curating heterozygous diploid genome assemblies (for instance when assembling using FALCON or FALCON-unzip).<\/p>\n<!-- Time to render link large description section of link id 24051: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24051: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24051: 0.00027108192443848 --> \n<tr><td><a href=\"https:\/\/github.com\/luidale\/pybam\" id=\"link-25088\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pybam<\/a>\n<!-- Time to render name section of link id 25088: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Very simple, pure python, BAM file reader. If you do not need to use BAM indexes, pybam is probably the fastest and simplest BAM parser out there, particularly if run under PyPy.<\/p>\n<!-- Time to render link large description section of link id 25088: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pybam> How to use <\/a>\n<!-- Time to render notes section of link id 25088: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25088: 0.00027894973754883 --> \n<tr><td><a href=\"https:\/\/www.jetbrains.com\/pycharm\/\" id=\"link-23890\" class=\"track_this_link \" rel=\"noopener noreferrer\">PyCharm<\/a>\n<!-- Time to render name section of link id 23890: 4.0531158447266E-6 --> \n<\/td>\n<td><p>PyCharm is a dedicated Python and Django IDE providing a wide range of essential tools for Python developers, tightly integrated together to create a convenient environment for productive Python development and Web development.<\/p>\n<!-- Time to render link large description section of link id 23890: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23890: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23890: 0.00028586387634277 --> \n<tr><td><a href=\"https:\/\/github.com\/epi2me-labs\/pychopper\" id=\"link-25702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pychopper<\/a>\n<!-- Time to render name section of link id 25702: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.<\/p>\n<!-- Time to render link large description section of link id 25702: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pychopper> How to use <\/a>\n<!-- Time to render notes section of link id 25702: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25702: 0.00028800964355469 --> \n<tr><td><a href=\"https:\/\/github.com\/a-slide\/pycoQC\" id=\"link-24034\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pycoQC<\/a>\n<!-- Time to render name section of link id 24034: 2.8610229492188E-6 --> \n<\/td>\n<td><p>pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore\/Guppy)<\/p>\n<!-- Time to render link large description section of link id 24034: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pycoQC> How to use <\/a>\n<!-- Time to render notes section of link id 24034: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24034: 0.00020599365234375 --> \n<tr><td><a href=\"https:\/\/github.com\/jiaaro\/pydub\" id=\"link-25647\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pydub<\/a>\n<!-- Time to render name section of link id 25647: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Manipulate audio with a simple and easy high level interface.<\/p>\n<!-- Time to render link large description section of link id 25647: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pydub> How to use <\/a>\n<!-- Time to render notes section of link id 25647: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25647: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/bvalot\/pyMLST\" id=\"link-24470\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pyMLST<\/a>\n<!-- Time to render name section of link id 24470: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Python Mlst Local Search Tool.<\/p>\n<!-- Time to render link large description section of link id 24470: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pyMLST> How to use <\/a>\n<!-- Time to render notes section of link id 24470: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24470: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/gbouras13\/pypolca\" id=\"link-25451\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pypolca<\/a>\n<!-- Time to render name section of link id 25451: 1.9073486328125E-6 --> \n<\/td>\n<td><p>pypolca is a Standalone Python re-implementation of the POLCA polisher from the MaSuRCA genome assembly and analysis toolkit.<\/p>\n<!-- Time to render link large description section of link id 25451: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pypolca> How to use <\/a>\n<!-- Time to render notes section of link id 25451: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25451: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/www.pypy.org\" id=\"link-24992\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PyPy<\/a>\n<!-- Time to render name section of link id 24992: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast, compliant alternative implementation of Python.<\/p>\n<!-- Time to render link large description section of link id 24992: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PyPy> How to use <\/a>\n<!-- Time to render notes section of link id 24992: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24992: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenmethods\/pyrho\" id=\"link-25294\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pyrho<\/a>\n<!-- Time to render name section of link id 25294: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast demography-aware inference of fine-scale recombination rates based on fused-LASSO.<\/p>\n<!-- Time to render link large description section of link id 25294: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pyrho> How to use <\/a>\n<!-- Time to render notes section of link id 25294: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25294: 0.00017881393432617 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/genotoul-bioinfo\/pyrocleaner\" id=\"link-24471\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PyroCleaner<\/a>\n<!-- Time to render name section of link id 24471: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PyroCleaner is intended to clean reads coming from pyrosequencing in order to ease the assembly process.<\/p>\n<!-- Time to render link large description section of link id 24471: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24471: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24471: 0.00018692016601562 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/pysam\" id=\"link-23702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pysam<\/a>\n<!-- Time to render name section of link id 23702: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the <a href=\"http:\/\/samtools.sourceforge.net\/\" rel=\"nofollow\">samtools<\/a> C-API.<\/p>\n<!-- Time to render link large description section of link id 23702: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23702: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23702: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/alimanfoo\/pysamstats\" id=\"link-26218\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pysamstats<\/a>\n<!-- Time to render name section of link id 26218: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file.<\/p>\n<!-- Time to render link large description section of link id 26218: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pysamstats> How to use <\/a>\n<!-- Time to render notes section of link id 26218: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26218: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/mgalardini\/pyseer\" id=\"link-25654\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pyseer<\/a>\n<!-- Time to render name section of link id 25654: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Sequence Element Enrichment Analysis (SEER), python implementation. Pyseer uses linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population on a phenotype of interest, while accounting for potentially very strong confounding population structure. This allows for genome-wide association studies (GWAS) to be performed in clonal organisms such as bacteria and viruses.<\/p>\n<!-- Time to render link large description section of link id 25654: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pyseer> How to use <\/a>\n<!-- Time to render notes section of link id 25654: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25654: 0.0002140998840332 --> \n<tr><td><a href=\"https:\/\/github.com\/PySlurm\/pyslurm\" id=\"link-24070\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PySlurm<\/a>\n<!-- Time to render name section of link id 24070: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This module provides a low-level Python wrapper around the Slurm C-API using Cython.<\/p>\n<!-- Time to render link large description section of link id 24070: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24070: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24070: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/github.com\/freezer333\/qgrs-cpp\" id=\"link-24473\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">qgrs-cpp<\/a>\n<!-- Time to render name section of link id 24473: 1.9073486328125E-6 --> \n<\/td>\n<td><p>C++ implementation of QGRS mapping algorithm (QGRS Mapper is a software program that generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences.)<\/p>\n<!-- Time to render link large description section of link id 24473: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24473: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24473: 0.00016593933105469 --> \n<tr><td><a href=\"https:\/\/qiime2.org\/\" id=\"link-23703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">QIIME<\/a>\n<!-- Time to render name section of link id 23703: 2.1457672119141E-6 --> \n<\/td>\n<td><p>QIIME (pronounced \"chime\") stands for Quantitative Insights Into ttMicrobial Ecology. QIIME is an open source software package for ttcomparison and analysis of microbial communities, primarily based on tthigh-throughput amplicon sequencing data (such as SSU rRNA) generated tton a variety of platforms, but also supporting analysis of other types ttof data (such as shotgun metagenomic data). QIIME takes users from tttheir raw sequencing output through initial analyses such as OTU ttpicking, taxonomic assignment, and construction of phylogenetic trees ttfrom representative sequences of OTUs, and through downstream ttstatistical analysis, visualization, and production of ttpublication-quality graphics. QIIME has been applied to single studies ttbased on billions of sequences from thousands of samples. ttttt<\/p>\n<!-- Time to render link large description section of link id 23703: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_QIIME> How to use <\/a>\n<!-- Time to render notes section of link id 23703: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23703: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/r-loop.org\/?pg=qmrlfs\" id=\"link-24107\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">QmRLFS-finder<\/a>\n<!-- Time to render name section of link id 24107: 2.1457672119141E-6 --> \n<\/td>\n<td><p>QmRLFS-finder, the first R-loop finding tool which uses (unsupervised) QmRLFS (Quantitative Models of RLFS) models to predict RLFSs. This command line tool generates locations and detailed information of RLFSs as well as standards-compliant output files for further analysis and visualization.<\/p>\n<!-- Time to render link large description section of link id 24107: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_QmRLFS-finder> How to use <\/a>\n<!-- Time to render notes section of link id 24107: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24107: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/TCLamnidis\/qpWrapper\" id=\"link-24474\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">qpWrapper<\/a>\n<!-- Time to render name section of link id 24474: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tools allowing to launch qpAdmn analyzes (Admixtools) in series on a list of individuals.<\/p>\n<!-- Time to render link large description section of link id 24474: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24474: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24474: 0.0001671314239502 --> \n<tr><td><a href=\"http:\/\/www.cbcb.umd.edu\/software\/quake\/\" id=\"link-23704\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Quake<\/a>\n<!-- Time to render name section of link id 23704: 4.0531158447266E-6 --> \n<\/td>\n<td><div class=\"content\">t Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. &gt;15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections, which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.<\/div>\n<!-- Time to render link large description section of link id 23704: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Quake> How to use <\/a>\n<!-- Time to render notes section of link id 23704: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23704: 0.00031399726867676 --> \n<tr><td><a href=\"http:\/\/qualimap.bioinfo.cipf.es\/\" id=\"link-23705\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Qualimap<\/a>\n<!-- Time to render name section of link id 23705: 2.8610229492188E-6 --> \n<\/td>\n<td><p><b>Qualimap 2<\/b> is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.<\/p>\n<!-- Time to render link large description section of link id 23705: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Qualimap> How to use <\/a>\n<!-- Time to render notes section of link id 23705: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23705: 0.00023794174194336 --> \n<tr><td><a href=\"https:\/\/github.com\/ctlab\/quant3p\" id=\"link-24475\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quant3p<\/a>\n<!-- Time to render name section of link id 24475: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A set of scripts for 3' RNA-seq quantification.<\/p>\n<!-- Time to render link large description section of link id 24475: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_quant3p> How to use <\/a>\n<!-- Time to render notes section of link id 24475: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24475: 0.0002291202545166 --> \n<tr><td><a href=\"https:\/\/github.com\/aaranyue\/quarTeT\" id=\"link-25192\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quarTeT<\/a>\n<!-- Time to render name section of link id 25192: 5.0067901611328E-6 --> \n<\/td>\n<td><p>quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.<\/p>\n<!-- Time to render link large description section of link id 25192: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_quarTeT> How to use <\/a>\n<!-- Time to render notes section of link id 25192: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25192: 0.00038599967956543 --> \n<tr><td><a href=\"https:\/\/quarto.org\" id=\"link-25413\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Quarto<\/a>\n<!-- Time to render name section of link id 25413: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Quarto is a software that compiles a markdown code to html, pdf, or many other formats. It is a successor of pandoc.<\/p>\n<!-- Time to render link large description section of link id 25413: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Quarto> How to use <\/a>\n<!-- Time to render notes section of link id 25413: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25413: 0.00030899047851562 --> \n<tr><td><a href=\"https:\/\/quast.sourceforge.net\" id=\"link-23706\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">QUAST<\/a>\n<!-- Time to render name section of link id 23706: 4.0531158447266E-6 --> \n<\/td>\n<td><p>QUAST evaluates genome assemblies by computing various metrics<\/p>\n<!-- Time to render link large description section of link id 23706: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_QUAST> How to use <\/a>\n<!-- Time to render notes section of link id 23706: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23706: 0.00031018257141113 --> \n<tr><td><a href=\"https:\/\/github.com\/pephco\/quickLD\" id=\"link-25289\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quickLD<\/a>\n<!-- Time to render name section of link id 25289: 4.0531158447266E-6 --> \n<\/td>\n<td><p>High-performance Computation of Linkage Disequilibrium on CPUs and GPUs.<\/p>\n<!-- Time to render link large description section of link id 25289: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_quickLD> How to use <\/a>\n<!-- Time to render notes section of link id 25289: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25289: 0.00028586387634277 --> \n<tr><td><a href=\"https:\/\/github.com\/mahulchak\/quickmerge\" id=\"link-23938\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quickmerge<\/a>\n<!-- Time to render name section of link id 23938: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies<\/p>\n<!-- Time to render link large description section of link id 23938: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23938: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23938: 0.00030207633972168 --> \n<tr><td><a href=\"https:\/\/github.com\/gmarcais\/Quorum\" id=\"link-24042\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Quorum<\/a>\n<!-- Time to render name section of link id 24042: 3.814697265625E-6 --> \n<\/td>\n<td><p>QuorUM (Quality Optimized Reads from the University of Maryland) is an error corrector for Illumina reads.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24042: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24042: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24042: 0.00033307075500488 --> \n<tr><td><a href=\"http:\/\/cran.r-project.org\/\" id=\"link-23707\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">R<\/a>\n<!-- Time to render name section of link id 23707: 4.0531158447266E-6 --> \n<\/td>\n<td><p>R is \"GNU S\", a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.<\/p>\n<!-- Time to render link large description section of link id 23707: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_R> How to use <\/a>\n<!-- Time to render notes section of link id 23707: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23707: 0.00030398368835449 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/R-scape\/\" id=\"link-24476\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">R-scape<\/a>\n<!-- Time to render name section of link id 24476: 4.0531158447266E-6 --> \n<\/td>\n<td><p>R-scape looks for evidence of a conserved RNA structure by measuring pairwise covariations observed in an input multiple sequence alignment. It analyzes all possible pairs, including those in your proposed structure (if you provide one).<\/p>\n<!-- Time to render link large description section of link id 24476: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24476: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24476: 0.00028395652770996 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/r8s\/\" id=\"link-24477\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">r8s<\/a>\n<!-- Time to render name section of link id 24477: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This package implements several methods to infer divergence times on a molecular phylogeny, using penalized likelihood, maximum likelihood and nonparametric rate smoothing methods. It also implements miscellaneous tree and character evolution models and tests.<\/p>\n<!-- Time to render link large description section of link id 24477: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24477: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24477: 0.00028395652770996 --> \n<tr><td><a href=\"https:\/\/github.com\/lbcb-sci\/ra\" id=\"link-23949\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ra<\/a>\n<!-- Time to render name section of link id 23949: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Ra is as a fast and easy to use assembler for raw reads generated by third generation sequencing.<\/p>\n<!-- Time to render link large description section of link id 23949: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23949: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23949: 0.00031113624572754 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Rebaler\" id=\"link-24478\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Rabaler<\/a>\n<!-- Time to render name section of link id 24478: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences.<\/p>\n<!-- Time to render link large description section of link id 24478: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24478: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24478: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/RabbitBio\/RabbitUniq\" id=\"link-24479\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RabbitUniq<\/a>\n<!-- Time to render name section of link id 24479: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Compute unique k-mer faster.<\/p>\n<!-- Time to render link large description section of link id 24479: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24479: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24479: 0.00018811225891113 --> \n<tr><td><a href=\"https:\/\/github.com\/RabbitBio\/RabbitV\" id=\"link-24480\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RabbitV<\/a>\n<!-- Time to render name section of link id 24480: 4.0531158447266E-6 --> \n<\/td>\n<td><p>RabbitV is a highly optimized and practical toolkit for the detection of viruses and microorganisms in sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24480: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24480: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24480: 0.00029993057250977 --> \n<tr><td><a href=\"https:\/\/github.com\/lbcb-sci\/racon\" id=\"link-23828\" class=\"track_this_link \" rel=\"noopener noreferrer\">Racon<\/a>\n<!-- Time to render name section of link id 23828: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Consensus module for raw de novo DNA assembly of long uncorrected reads.<\/p>\n<!-- Time to render link large description section of link id 23828: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Racon> How to use <\/a>\n<!-- Time to render notes section of link id 23828: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23828: 0.00045990943908691 --> \n<tr><td><a href=\"http:\/\/www1.montpellier.inra.fr\/CBGP\/software\/RADIS\/index.html\" id=\"link-23847\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RADIS<\/a>\n<!-- Time to render name section of link id 23847: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Analysis of RAD-seq data for InterSpecific phylogeny<\/p>\n<!-- Time to render link large description section of link id 23847: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23847: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23847: 0.00042510032653809 --> \n<tr><td><a href=\"https:\/\/github.com\/SexGenomicsToolkit\/radsex\" id=\"link-25704\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">radsex<\/a>\n<!-- Time to render name section of link id 25704: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Find sex signal in RAD-Sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25704: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_radsex> How to use <\/a>\n<!-- Time to render notes section of link id 25704: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25704: 0.00050806999206543 --> \n<tr><td><a href=\"https:\/\/github.com\/at-cg\/RAFT\" id=\"link-25101\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAFT<\/a>\n<!-- Time to render name section of link id 25101: 8.1062316894531E-6 --> \n<\/td>\n<td><p>RAFT (Repeat Aware Fragmentation Tool) is an algorithm designed to improve assembly quality by rescuing contained reads.<\/p>\r\n<p dir=\"auto\">RAFT breaks long reads into smaller sub-reads by following an algorithm described in our <a href=\"https:\/\/github.com\/at-cg\/RAFT#papers\">preprint<\/a>. The read fragmentation allows an OLC assembler to retain contained reads during string graph construction. When input reads have non-uniform lengths, retaining contained reads improves assembly contiguity and base-level accuracy. The inputs to RAFT include an error-corrected read file in FASTA\/FASTQ format and an all-vs-all alignment file in PAF format. It performs read fragmentation and outputs the fragmented reads in FASTA format.<\/p>\r\n<p dir=\"auto\">We recommend users to use\u00a0<a href=\"https:\/\/github.com\/chhylp123\/hifiasm\">hifiasm<\/a>\u00a0for the initial steps (read error correction, all-vs-all overlap computation) and also for the final step (assembly of fragmented reads). The assembly output format of hifiasm is described\u00a0<a href=\"https:\/\/hifiasm.readthedocs.io\/en\/latest\/interpreting-output.html#interpreting-output\" rel=\"nofollow\">here<\/a>.<\/p>\r\n<p dir=\"auto\"><em>The RAFT-hifiasm workflow is recommended for long accurate reads with non-uniform length distribution (e.g., ONT Duplex, or a mixture of ONT Duplex and HiFi reads). ONT UL reads can optionally be\u00a0<a href=\"https:\/\/github.com\/chhylp123\/hifiasm#ul\">integrated<\/a>\u00a0during the final assembly step.<\/em><\/p>\n<!-- Time to render link large description section of link id 25101: 1.9073486328125E-6 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAFT> How to use <\/a>\n<!-- Time to render notes section of link id 25101: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25101: 0.00055480003356934 --> \n<tr><td><a href=\"https:\/\/github.com\/malonge\/RaGOO\" id=\"link-24045\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RaGOO<\/a>\n<!-- Time to render name section of link id 24045: 8.1062316894531E-6 --> \n<\/td>\n<td><p>A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24045: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24045: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24045: 0.00052499771118164 --> \n<tr><td><a href=\"http:\/\/fenderglass.github.io\/Ragout\/\" id=\"link-23951\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ragout<\/a>\n<!-- Time to render name section of link id 23951: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references.<\/p>\n<!-- Time to render link large description section of link id 23951: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23951: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23951: 0.00052618980407715 --> \n<tr><td><a href=\"https:\/\/github.com\/malonge\/RagTag\" id=\"link-24481\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RagTag<\/a>\n<!-- Time to render name section of link id 24481: 6.9141387939453E-6 --> \n<\/td>\n<td><p>RagTag, the successor to RaGOO, is a command line tool for reference-guided genome assembly improvement.<\/p>\n<!-- Time to render link large description section of link id 24481: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RagTag> How to use <\/a>\n<!-- Time to render notes section of link id 24481: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24481: 0.00054597854614258 --> \n<tr><td><a href=\"https:\/\/github.com\/alachins\/raisd\" id=\"link-24482\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAiSD<\/a>\n<!-- Time to render name section of link id 24482: 2.8610229492188E-6 --> \n<\/td>\n<td><p>RAiSD (Raised Accuracy in Sweep Detection) is a stand-alone software implementation of the \u03bc statistic for selective sweep detection.<\/p>\n<!-- Time to render link large description section of link id 24482: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAiSD> How to use <\/a>\n<!-- Time to render notes section of link id 24482: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24482: 0.00024008750915527 --> \n<tr><td><a href=\"https:\/\/github.com\/TGAC\/RAMPART\" id=\"link-24483\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAMPART<\/a>\n<!-- Time to render name section of link id 24483: 4.0531158447266E-6 --> \n<\/td>\n<td><p>RAMPART is a configurable pipeline for de novo assembly of DNA sequence data. RAMPART is not a de novo assembler.<\/p>\n<!-- Time to render link large description section of link id 24483: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24483: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24483: 0.0002129077911377 --> \n<tr><td><a href=\"https:\/\/github.com\/moeinzadeh\/Ranbow\" id=\"link-24484\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ranbow<\/a>\n<!-- Time to render name section of link id 24484: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Ranbow is a haplotype assembler for polyploid genomes.<\/p>\n<!-- Time to render link large description section of link id 24484: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24484: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24484: 0.00022602081298828 --> \n<tr><td><a href=\"http:\/\/bioinformatics.psb.ugent.be\/supplementary_data\/erbon\/nov2003\/\" id=\"link-23907\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">randfold<\/a>\n<!-- Time to render name section of link id 23907: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The software compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences..<\/p>\n<!-- Time to render link large description section of link id 23907: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_randfold> How to use <\/a>\n<!-- Time to render notes section of link id 23907: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23907: 0.00021100044250488 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/bsblabludwig\/rastair\/src\/master\/\" id=\"link-25551\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rastair<\/a>\n<!-- Time to render name section of link id 25551: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Fast processing of TET-assisted pyridine borane sequencing (TAPS)-based sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25551: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rastair> How to use <\/a>\n<!-- Time to render notes section of link id 25551: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25551: 0.00021100044250488 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/Ratatosk\" id=\"link-24485\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ratatosk<\/a>\n<!-- Time to render name section of link id 24485: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Ratatosk is a phased error correction tool for erroneous long reads based on compacted and colored de Bruijn graphs built from accurate short reads.<\/p>\n<!-- Time to render link large description section of link id 24485: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24485: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24485: 0.00021100044250488 --> \n<tr><td><a href=\"http:\/\/ratt.sourceforge.net\/index.html\" id=\"link-23884\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RATT<\/a>\n<!-- Time to render name section of link id 23884: 2.8610229492188E-6 --> \n<\/td>\n<td><p>RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.<\/p>\n<!-- Time to render link large description section of link id 23884: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23884: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23884: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/stamatak\/standard-RAxML\" id=\"link-23708\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAxML<\/a>\n<!-- Time to render name section of link id 23708: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.<\/p>\n<!-- Time to render link large description section of link id 23708: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAxML> How to use <\/a>\n<!-- Time to render notes section of link id 23708: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23708: 0.00020694732666016 --> \n<tr><td><a href=\"https:\/\/github.com\/amkozlov\/raxml-ng\" id=\"link-24003\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAxML-NG<\/a>\n<!-- Time to render name section of link id 24003: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.<\/p>\n<!-- Time to render link large description section of link id 24003: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAxML-NG> How to use <\/a>\n<!-- Time to render notes section of link id 24003: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24003: 0.0002131462097168 --> \n<tr><td><a href=\"https:\/\/github.com\/noahares\/raxtax\" id=\"link-25810\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">raxtax<\/a>\n<!-- Time to render name section of link id 25810: 3.0994415283203E-6 --> \n<\/td>\n<td><p>raxtax is a fast and efficient k-mer-based non-Bayesian taxonomic classifier for barcoding DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 25810: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_raxtax> How to use <\/a>\n<!-- Time to render notes section of link id 25810: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25810: 0.00022101402282715 --> \n<tr><td><a href=\"http:\/\/denovoassembler.sourceforge.net\/download.html\" id=\"link-23709\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ray<\/a>\n<!-- Time to render name section of link id 23709: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Assemble genomes in parallel using the message-passing interface<\/p>\n<!-- Time to render link large description section of link id 23709: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23709: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23709: 0.00021219253540039 --> \n<tr><td><a href=\"https:\/\/www.rdkit.org\" id=\"link-26148\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDKit<\/a>\n<!-- Time to render name section of link id 26148: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.<\/p>\n<!-- Time to render link large description section of link id 26148: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RDKit> How to use <\/a>\n<!-- Time to render notes section of link id 26148: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26148: 0.00022196769714355 --> \n<tr><td><a href=\"http:\/\/sourceforge.net\/projects\/rdp-classifier\/\" id=\"link-23710\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDP Classifier<\/a>\n<!-- Time to render name section of link id 23710: 3.0994415283203E-6 --> \n<\/td>\n<td><div>The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.<\/div>\n<!-- Time to render link large description section of link id 23710: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23710: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23710: 0.00021100044250488 --> \n<tr><td><a href=\"https:\/\/github.com\/rdpstaff\/RDPTools\" id=\"link-23712\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDPTools<\/a>\n<!-- Time to render name section of link id 23712: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Collection of commonly used RDP Tools for easy building<\/p>\n<!-- Time to render link large description section of link id 23712: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RDPTools> How to use <\/a>\n<!-- Time to render notes section of link id 23712: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23712: 0.0002138614654541 --> \n<tr><td><a href=\"https:\/\/github.com\/dimitris-karapliafis\/RdRpCATCH\" id=\"link-25763\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RdRpCATCH<\/a>\n<!-- Time to render name section of link id 25763: 2.1457672119141E-6 --> \n<\/td>\n<td>A community effort to create a shared resource for HMM-based RdRp discovery \n<!-- Time to render link large description section of link id 25763: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RdRpCATCH> How to use <\/a>\n<!-- Time to render notes section of link id 25763: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25763: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/rdxplorer.sourceforge.net\/\" id=\"link-25313\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDXplorer<\/a>\n<!-- Time to render name section of link id 25313: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The RDXplorer (Read Depth eXplorer) is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.<\/p>\n<!-- Time to render link large description section of link id 25313: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RDXplorer> How to use <\/a>\n<!-- Time to render notes section of link id 25313: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25313: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/tguenther\/read\/src\/master\/\" id=\"link-25146\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">READ<\/a>\n<!-- Time to render name section of link id 25146: 3.0994415283203E-6 --> \n<\/td>\n<td><p>READ is a method to infer the degree of relationship (up to second degree, i.e. nephew\/niece-uncle\/aunt, grandparent-grandchild or half-siblings) for a pair of low-coverage individuals.<\/p>\n<!-- Time to render link large description section of link id 25146: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_READ> How to use <\/a>\n<!-- Time to render notes section of link id 25146: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25146: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/DessimozLab\/read2tree\" id=\"link-24959\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">read2tree<\/a>\n<!-- Time to render name section of link id 24959: 1.9073486328125E-6 --> \n<\/td>\n<td><p>read2tree is a software tool that allows to obtain alignment matrices for tree inference.<\/p>\n<!-- Time to render link large description section of link id 24959: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_read2tree> How to use <\/a>\n<!-- Time to render notes section of link id 24959: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24959: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/GuntherLab\/READv2\" id=\"link-25546\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">READv2<\/a>\n<!-- Time to render name section of link id 25546: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Relationship Estimation from Ancient DNA version 2.<\/p>\n<!-- Time to render link large description section of link id 25546: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_READv2> How to use <\/a>\n<!-- Time to render notes section of link id 25546: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25546: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/www.sanger.ac.uk\/resources\/software\/reapr\/#t_2)\" id=\"link-23713\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REAPR<\/a>\n<!-- Time to render name section of link id 23713: 2.1457672119141E-6 --> \n<\/td>\n<td><p>REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.<\/p>\n<!-- Time to render link large description section of link id 23713: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23713: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23713: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/khyox\/recentrifuge\" id=\"link-25784\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Recentrifuge<\/a>\n<!-- Time to render name section of link id 25784: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Robust comparative analysis and contamination removal for metagenomics<\/p>\n<!-- Time to render link large description section of link id 25784: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Recentrifuge> How to use <\/a>\n<!-- Time to render notes section of link id 25784: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25784: 0.00018310546875 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/software\/recon\/\" id=\"link-23924\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RECON<\/a>\n<!-- Time to render name section of link id 23924: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A package for automated de novo identification of repeat families from genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 23924: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RECON> How to use <\/a>\n<!-- Time to render notes section of link id 23924: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23924: 0.00017213821411133 --> \n<tr><td><a href=\"http:\/\/srv00.recas.ba.infn.it\/reditools\/\" id=\"link-23975\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REDItools<\/a>\n<!-- Time to render name section of link id 23975: 3.0994415283203E-6 --> \n<\/td>\n<td><p>REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23975: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23975: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23975: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/lpryszcz\/redundans\" id=\"link-23840\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Redundans<\/a>\n<!-- Time to render name section of link id 23840: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Redundans is a pipeline that assists an assembly of heterozygous\/polymorphic genomes.<\/p>\n<!-- Time to render link large description section of link id 23840: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23840: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23840: 0.00017189979553223 --> \n<tr><td><a href=\"https:\/\/github.com\/cpouchon\/REFMAKER\" id=\"link-25264\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REFMAKER<\/a>\n<!-- Time to render name section of link id 25264: 1.9073486328125E-6 --> \n<\/td>\n<td><p>REFMAKER is a command-line and user-friendly pipeline providing different tools to create nuclear references from genomic assemblies of shotgun libraries.<\/p>\n<!-- Time to render link large description section of link id 25264: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REFMAKER> How to use <\/a>\n<!-- Time to render notes section of link id 25264: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25264: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/rgcgithub.github.io\/regenie\/\" id=\"link-26198\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">regenie<\/a>\n<!-- Time to render name section of link id 26198: 1.9073486328125E-6 --> \n<\/td>\n<td><p>regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.<\/p>\n<!-- Time to render link large description section of link id 26198: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_regenie> How to use <\/a>\n<!-- Time to render notes section of link id 26198: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26198: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/griffithlab\/regtools\" id=\"link-24487\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RegTools<\/a>\n<!-- Time to render name section of link id 24487: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.<\/p>\n<!-- Time to render link large description section of link id 24487: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24487: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24487: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/kr-colab\/ReLERNN\" id=\"link-24489\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ReLERNN<\/a>\n<!-- Time to render name section of link id 24489: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Recombination Landscape Estimation using Recurrent Neural Networks<\/p>\n<!-- Time to render link large description section of link id 24489: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ReLERNN> How to use <\/a>\n<!-- Time to render notes section of link id 24489: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24489: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfomaticsCSU\/RepAHR\" id=\"link-24490\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepAHR<\/a>\n<!-- Time to render name section of link id 24490: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RepAHR is used to identify repeats(repetitive sequences) in genome using Next-Generation Sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24490: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24490: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24490: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/simoncchu\/REPdenovo\" id=\"link-24491\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REPdenovo<\/a>\n<!-- Time to render name section of link id 24491: 1.9073486328125E-6 --> \n<\/td>\n<td><p>REPdenovo is designed for constructing repeats directly from sequence (paired-end) reads. It based on the idea of frequent k-mer assembly. REPdenovo provides many functionalities, and can generate much longer repeats than existing tools. Internally, REPdenovo uses Jellyfish for k-mer counting, Velvet for assembly, and bwa to map reads on the Transposable Elements.<\/p>\n<!-- Time to render link large description section of link id 24491: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24491: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24491: 0.00018787384033203 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/petrnovak\/repex_tarean\/src\/devel\/\" id=\"link-24492\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatExplorer<\/a>\n<!-- Time to render name section of link id 24492: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes.<\/p>\n<!-- Time to render link large description section of link id 24492: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24492: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24492: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/www.repeatmasker.org\/\" id=\"link-23714\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatMasker<\/a>\n<!-- Time to render name section of link id 23714: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RepeatMasker is a program that screens DNA sequences for interspersed repeats (thanks to RepBase repeats databanks specially formatted) and low complexity DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 23714: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RepeatMasker> How to use <\/a>\n<!-- Time to render notes section of link id 23714: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23714: 0.00018405914306641 --> \n<tr><td><a href=\"http:\/\/www.repeatmasker.org\/RepeatModeler.html\" id=\"link-23715\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatModeler<\/a>\n<!-- Time to render name section of link id 23715: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RepeatModeler is a de-novo repeat family identification and modeling package.<\/p>\n<!-- Time to render link large description section of link id 23715: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RepeatModeler> How to use <\/a>\n<!-- Time to render notes section of link id 23715: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23715: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/Dfam-consortium\/RepeatScout\" id=\"link-23716\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatScout<\/a>\n<!-- Time to render name section of link id 23716: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RepeatScout is a tool to discover repetitive substrings in DNA.<\/p>\n<!-- Time to render link large description section of link id 23716: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RepeatScout> How to use <\/a>\n<!-- Time to render notes section of link id 23716: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23716: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/github.com\/nerettilab\/RepEnrich2\" id=\"link-24024\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepEnrich2<\/a>\n<!-- Time to render name section of link id 24024: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24024: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24024: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24024: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/urgi.versailles.inra.fr\/Tools\/REPET\" id=\"link-23717\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REPET<\/a>\n<!-- Time to render name section of link id 23717: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The<b>\u00a0REPET <\/b><b>package<\/b> (t Flutre <i>et al<\/i>, 2011 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale.<\/p>\n<!-- Time to render link large description section of link id 23717: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REPET> How to use <\/a>\n<!-- Time to render notes section of link id 23717: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23717: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/github.com\/Vicky123wzy\/RetroScan\" id=\"link-24494\" class=\"track_this_link \" rel=\"noopener noreferrer\">RetroScan<\/a>\n<!-- Time to render name section of link id 24494: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RetroScan is an easy-to-use tool for retrocopy identification that integrates a series of bioinformatics tools (LAST, BEDtools, ClustalW2, KaKs_Calculator, HISAT2, StringTie, SAMtools and Shiny) and scripts.<\/p>\n<!-- Time to render link large description section of link id 24494: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RetroScan> How to use <\/a>\n<!-- Time to render notes section of link id 24494: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24494: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/github.com\/tk2\/RetroSeq\" id=\"link-24049\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RetroSeq<\/a>\n<!-- Time to render name section of link id 24049: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.<\/p>\n<!-- Time to render link large description section of link id 24049: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24049: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24049: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/revbayes.github.io\/\" id=\"link-24018\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RevBayes<\/a>\n<!-- Time to render name section of link id 24018: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. However, the environment is quite general and can be useful for many complex modeling tasks.<\/p>\n<!-- Time to render link large description section of link id 24018: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24018: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24018: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/REViewer\" id=\"link-25729\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REViewer<\/a>\n<!-- Time to render name section of link id 25729: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool for visualizing alignments of reads in regions containing tandem repeats<\/p>\n<!-- Time to render link large description section of link id 25729: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REViewer> How to use <\/a>\n<!-- Time to render notes section of link id 25729: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25729: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/slowkoni\/rfmix\" id=\"link-23770\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RFMIX<\/a>\n<!-- Time to render name section of link id 23770: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A discriminative method for local ancestry inference<\/p>\n<!-- Time to render link large description section of link id 23770: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rfmix> How to use <\/a>\n<!-- Time to render notes section of link id 23770: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23770: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/www.ncrna.org\/softwares\/rfold\/\" id=\"link-24495\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Rfold<\/a>\n<!-- Time to render name section of link id 24495: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Rfold computes local base pairing probabilities for long DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 24495: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24495: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24495: 0.00016283988952637 --> \n<tr><td><a href=\"https:\/\/github.com\/aldertzomer\/RFPlasmid\" id=\"link-25063\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RFPlasmid<\/a>\n<!-- Time to render name section of link id 25063: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RFPlasmid predicts plasmid contigs from assemblies using single copy marker genes, plasmid genes, and kmers.<\/p>\n<!-- Time to render link large description section of link id 25063: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RFPlasmid> How to use <\/a>\n<!-- Time to render notes section of link id 25063: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25063: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/arpcard\/rgi\" id=\"link-24497\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RGI<\/a>\n<!-- Time to render name section of link id 24497: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.<\/p>\n<!-- Time to render link large description section of link id 24497: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RGI> How to use <\/a>\n<!-- Time to render notes section of link id 24497: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24497: 0.00019121170043945 --> \n<tr><td><a href=\"https:\/\/ohlerlab.mdc-berlin.de\/software\/RiboTaper_126\/\" id=\"link-24041\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RiboTaper<\/a>\n<!-- Time to render name section of link id 24041: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.<\/p>\n<!-- Time to render link large description section of link id 24041: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24041: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24041: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/BurntSushi\/ripgrep\" id=\"link-25733\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ripgrep<\/a>\n<!-- Time to render name section of link id 25733: 2.8610229492188E-6 --> \n<\/td>\n<td><p>ripgrep is a line-oriented search tool that recursively searches the current directory for a regex pattern.<\/p>\n<!-- Time to render link large description section of link id 25733: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ripgrep> How to use <\/a>\n<!-- Time to render notes section of link id 25733: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25733: 0.00019121170043945 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/rnaseq-mats\/\" id=\"link-23981\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rMATS<\/a>\n<!-- Time to render name section of link id 23981: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns.<\/p>\n<!-- Time to render link large description section of link id 23981: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23981: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23981: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/Xinglab\/rmats-turbo\" id=\"link-24498\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rMATS turbo<\/a>\n<!-- Time to render name section of link id 24498: 3.0994415283203E-6 --> \n<\/td>\n<td><p>rMATS turbo is the C\/Cython version of rMATS (refer to http:\/\/rnaseq-mats.sourceforge.net) : Multivariate Analysis of Transcript Splicing (MATS). The major difference between rMATS turbo and rMATS is speed and space usage.<\/p>\n<!-- Time to render link large description section of link id 24498: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rMATS_turbo> How to use <\/a>\n<!-- Time to render notes section of link id 24498: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24498: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/www.repeatmasker.org\/RMBlast.html\" id=\"link-23718\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RMBlast<\/a>\n<!-- Time to render name section of link id 23718: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program \"rmblastn\" for use with RepeatMasker and RepeatModeler. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:<br \/>\r\n<br \/>\r\n\u00a0\u00a0 - Support for custom matrices ( without KA-Statistics ).<br \/>\r\n\u00a0\u00a0\u00a0 - Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.<br \/>\r\n\u00a0\u00a0\u00a0 - Support for cross_match-like masklevel filtering.<\/p>\n<!-- Time to render link large description section of link id 23718: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rmblast-2.13.0> How to use <\/a>\n<!-- Time to render notes section of link id 23718: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23718: 0.00017380714416504 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-leipzig.de\/~kristin\/Software\/RNAclust\/\" id=\"link-24499\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAclust<\/a>\n<!-- Time to render name section of link id 24499: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif.<\/p>\n<!-- Time to render link large description section of link id 24499: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24499: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24499: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/services.healthtech.dtu.dk\/services\/RNAmmer-1.2\/\" id=\"link-23719\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAmmer<\/a>\n<!-- Time to render name section of link id 23719: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Rnammer predicts 5s\/8s, 16s\/18s, and 23s\/28s ribosomal RNA in tttfull genome sequences. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project.<\/p>\n<!-- Time to render link large description section of link id 23719: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RNAmmer> How to use <\/a>\n<!-- Time to render notes section of link id 23719: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23719: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-freiburg.de\/Software\/RNAscClust\/\" id=\"link-24500\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAscClust<\/a>\n<!-- Time to render name section of link id 24500: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RNAscClust is a pipeline to cluster a set of structured RNAs taking their respective structural conservation into account. The aim of RNAscClust is to aid the discovery of families and classes of ncRNAs.<\/p>\n<!-- Time to render link large description section of link id 24500: 0.00029921531677246 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24500: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24500: 0.00049400329589844 --> \n<tr><td><a href=\"https:\/\/www.tbi.univie.ac.at\/software\/RNAz\/\" id=\"link-24501\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAz<\/a>\n<!-- Time to render name section of link id 24501: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RNAz detects stable and conserved RNA secondary structures in multiple sequence alignments.<\/p>\n<!-- Time to render link large description section of link id 24501: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24501: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24501: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/sanger-pathogens.github.io\/Roary\/\" id=\"link-23809\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Roary<\/a>\n<!-- Time to render name section of link id 23809: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.<\/p>\n<!-- Time to render link large description section of link id 23809: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Roary> How to use <\/a>\n<!-- Time to render notes section of link id 23809: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23809: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/github.com\/aberer\/RogueNaRok\" id=\"link-24502\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RogueNaRok<\/a>\n<!-- Time to render name section of link id 24502: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A versatile and scalable algorithm for rogue taxon identification.<\/p>\n<!-- Time to render link large description section of link id 24502: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24502: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24502: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/ROHan\" id=\"link-24503\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ROHan<\/a>\n<!-- Time to render name section of link id 24503: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity.<\/p>\n<!-- Time to render link large description section of link id 24503: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ROHan> How to use <\/a>\n<!-- Time to render notes section of link id 24503: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24503: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/ropebwt2\" id=\"link-25113\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RopeBWT2<\/a>\n<!-- Time to render name section of link id 25113: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 25113: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RopeBWT2> How to use <\/a>\n<!-- Time to render notes section of link id 25113: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25113: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/ternaris\/rosbags\" id=\"link-25900\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rosbags<\/a>\n<!-- Time to render name section of link id 25900: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Rosbags is the pure python library for everything rosbag.<\/p>\n<!-- Time to render link large description section of link id 25900: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rosbags> How to use <\/a>\n<!-- Time to render notes section of link id 25900: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25900: 0.00018215179443359 --> \n<tr><td><a href=\"http:\/\/younglab.wi.mit.edu\/super_enhancer_code.html\" id=\"link-24504\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ROSE<\/a>\n<!-- Time to render name section of link id 24504: 2.1457672119141E-6 --> \n<\/td>\n<td><p>To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)<\/p>\n<!-- Time to render link large description section of link id 24504: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ROSE> How to use <\/a>\n<!-- Time to render notes section of link id 24504: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24504: 0.0001828670501709 --> \n<tr><td><a href=\"http:\/\/smithlabresearch.org\/software\/rseg\/\" id=\"link-24505\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RSEG<\/a>\n<!-- Time to render name section of link id 24505: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers.<\/p>\n<!-- Time to render link large description section of link id 24505: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24505: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24505: 0.00017690658569336 --> \n<tr><td><a href=\"http:\/\/deweylab.github.io\/RSEM\/\" id=\"link-23877\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RSEM<\/a>\n<!-- Time to render name section of link id 23877: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RSEM (RNA-Seq by Expectation-Maximization) is a software package for estimating gene and isoform expression levels from RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 23877: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RSEM> How to use <\/a>\n<!-- Time to render notes section of link id 23877: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23877: 0.00018787384033203 --> \n<tr><td><a href=\"http:\/\/rseqc.sourceforge.net\/\" id=\"link-23720\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RSeQC<\/a>\n<!-- Time to render name section of link id 23720: 5.0067901611328E-6 --> \n<\/td>\n<td><p>RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data<\/p>\n<!-- Time to render link large description section of link id 23720: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RSeQC> How to use <\/a>\n<!-- Time to render notes section of link id 23720: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23720: 0.00038313865661621 --> \n<tr><td><a href=\"https:\/\/github.com\/RealTimeGenomics\/rtg-tools\" id=\"link-26164\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RTGTools<\/a>\n<!-- Time to render name section of link id 26164: 5.0067901611328E-6 --> \n<\/td>\n<td><p>RTG Tools is a subset of\u00a0<a href=\"https:\/\/github.com\/RealTimeGenomics\/rtg-core\">RTG Core<\/a>\u00a0that includes several useful utilities for dealing with VCF files and sequence data. Probably the most interesting is the\u00a0<code>vcfeval<\/code>\u00a0command which performs sophisticated comparison of VCF files.<\/p>\n<!-- Time to render link large description section of link id 26164: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RTGTools> How to use <\/a>\n<!-- Time to render notes section of link id 26164: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26164: 0.00034689903259277 --> \n<tr><td><a href=\"https:\/\/www.ruby-lang.org\/en\/\" id=\"link-23899\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ruby<\/a>\n<!-- Time to render name section of link id 23899: 7.8678131103516E-6 --> \n<\/td>\n<td><p>A dynamic, open source programming language.<\/p>\n<!-- Time to render link large description section of link id 23899: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ruby> How to use <\/a>\n<!-- Time to render notes section of link id 23899: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23899: 0.00058293342590332 --> \n<tr><td><a href=\"https:\/\/github.com\/shenwei356\/rush\" id=\"link-25734\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rush<\/a>\n<!-- Time to render name section of link id 25734: 7.8678131103516E-6 --> \n<\/td>\n<td><p>A cross-platform command-line tool for executing jobs in parallel.<\/p>\n<!-- Time to render link large description section of link id 25734: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rush> How to use <\/a>\n<!-- Time to render notes section of link id 25734: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25734: 0.00052595138549805 --> \n<tr><td><a href=\"https:\/\/github.com\/ekimb\/rust-mdbg\" id=\"link-24506\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rust-mdbg<\/a>\n<!-- Time to render name section of link id 24506: 6.9141387939453E-6 --> \n<\/td>\n<td><p>rust-mdbg is an ultra-fast minimizer-space de Bruijn graph (mdBG) implementation, geared towards the assembly of long and accurate reads such as PacBio HiFi.<\/p>\n<!-- Time to render link large description section of link id 24506: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rust-mdbg> How to use <\/a>\n<!-- Time to render notes section of link id 24506: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24506: 0.00051283836364746 --> \n<tr><td><a href=\"https:\/\/github.com\/guanjue\/S3V2_IDEAS_ESMP\" id=\"link-24507\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">S3V2_IDEAS_ESMP<\/a>\n<!-- Time to render name section of link id 24507: 7.1525573730469E-6 --> \n<\/td>\n<td><p>A package for normalizing, denoising and integrating epigenomic datasets across different cell types.<\/p>\n<!-- Time to render link large description section of link id 24507: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24507: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24507: 0.00050997734069824 --> \n<tr><td><a href=\"https:\/\/github.com\/najoshi\/sabre\" id=\"link-23835\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sabre<\/a>\n<!-- Time to render name section of link id 23835: 3.814697265625E-6 --> \n<\/td>\n<td><p>A barcode demultiplexing and trimming tool for FastQ files.<\/p>\n<!-- Time to render link large description section of link id 23835: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23835: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23835: 0.00024795532226562 --> \n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/salmon\" id=\"link-23776\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Salmon<\/a>\n<!-- Time to render name section of link id 23776: 3.814697265625E-6 --> \n<\/td>\n<td><p>Highly-accurate &amp; wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments<\/p>\n<!-- Time to render link large description section of link id 23776: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Salmon> How to use <\/a>\n<!-- Time to render notes section of link id 23776: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23776: 0.00090789794921875 --> \n<tr><td><a href=\"https:\/\/github.com\/machinegun\/SALSA\" id=\"link-24109\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SALSA<\/a>\n<!-- Time to render name section of link id 24109: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A tool to scaffold long read assemblies with Hi-C data<\/p>\n<!-- Time to render link large description section of link id 24109: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SALSA> How to use <\/a>\n<!-- Time to render notes section of link id 24109: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24109: 0.00025391578674316 --> \n<tr><td><a href=\"https:\/\/github.com\/biod\/sambamba\" id=\"link-23917\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sambamba<\/a>\n<!-- Time to render name section of link id 23917: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.<\/p>\n<!-- Time to render link large description section of link id 23917: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sambamba> How to use <\/a>\n<!-- Time to render notes section of link id 23917: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23917: 0.00024080276489258 --> \n<tr><td><a href=\"https:\/\/github.com\/GregoryFaust\/samblaster\" id=\"link-23829\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samblaster<\/a>\n<!-- Time to render name section of link id 23829: 3.0994415283203E-6 --> \n<\/td>\n<td><p>samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and\/or split read mappings to separate SAM files, and\/or unmapped\/clipped reads to a separate FASTQ file.<\/p>\n<!-- Time to render link large description section of link id 23829: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_samblaster> How to use <\/a>\n<!-- Time to render notes section of link id 23829: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23829: 0.00023913383483887 --> \n<tr><td><a href=\"https:\/\/github.com\/tseemann\/samclip\" id=\"link-24508\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samclip<\/a>\n<!-- Time to render name section of link id 24508: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Filter SAM file for soft and hard clipped alignments<\/p>\n<!-- Time to render link large description section of link id 24508: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24508: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24508: 0.00023818016052246 --> \n<tr><td><a href=\"http:\/\/samtools.sourceforge.net\/\" id=\"link-23721\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samtools<\/a>\n<!-- Time to render name section of link id 23721: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SAM (Sequence Alignment\/Map). SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.<\/p>\n<!-- Time to render link large description section of link id 23721: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_samtools> How to use <\/a>\n<!-- Time to render notes section of link id 23721: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23721: 0.00027894973754883 --> \n<tr><td><a href=\"https:\/\/github.com\/PF2-pasteur-fr\/SARTools\" id=\"link-23722\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SARTools<\/a>\n<!-- Time to render name section of link id 23722: 4.0531158447266E-6 --> \n<\/td>\n<td><p>SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files.<\/p>\n<!-- Time to render link large description section of link id 23722: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in R-4.5.0\n<!-- Time to render notes section of link id 23722: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23722: 0.00025701522827148 --> \n<tr><td><a href=\"http:\/\/satsuma.sourceforge.net\/\" id=\"link-24509\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Satsuma<\/a>\n<!-- Time to render name section of link id 24509: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Highly sensitive whole-genome synteny alignments.<\/p>\n<!-- Time to render link large description section of link id 24509: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24509: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24509: 0.00026297569274902 --> \n<tr><td><a href=\"http:\/\/www.genoscope.cns.fr\/externe\/saturn\/\" id=\"link-23960\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Saturn<\/a>\n<!-- Time to render name section of link id 23960: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A tool for assessing the library saturation without any reference genome. .<\/p>\n<!-- Time to render link large description section of link id 23960: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23960: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23960: 0.00023913383483887 --> \n<tr><td><a href=\"https:\/\/www.scala-sbt.org\/\" id=\"link-24039\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sbt<\/a>\n<!-- Time to render name section of link id 24039: 3.814697265625E-6 --> \n<\/td>\n<td><p>sbt is a build tool for Scala, Java, and more.<\/p>\n<!-- Time to render link large description section of link id 24039: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24039: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24039: 0.00023698806762695 --> \n<tr><td><a href=\"https:\/\/github.com\/wtsi-hpag\/Scaff10X\" id=\"link-24510\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scaff10X<\/a>\n<!-- Time to render name section of link id 24510: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads<\/p>\n<!-- Time to render link large description section of link id 24510: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24510: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24510: 0.00018620491027832 --> \n<tr><td><a href=\"http:\/\/blog.theseed.org\/servers\/2010\/07\/scan-for-matches.html\" id=\"link-23723\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scan For Matches<\/a>\n<!-- Time to render name section of link id 23723: 6.9141387939453E-6 --> \n<\/td>\n<td><p><b><\/b>scan_for_matches is a utility written in C for locating patterns in DNA or protein FASTA files.<\/p>\n<!-- Time to render link large description section of link id 23723: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23723: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23723: 0.00053501129150391 --> \n<tr><td><a href=\"https:\/\/github.com\/scverse\/scanpy\" id=\"link-25104\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scanpy<\/a>\n<!-- Time to render name section of link id 25104: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. \u00a0It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.<\/p>\n<!-- Time to render link large description section of link id 25104: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Scanpy> How to use <\/a>\n<!-- Time to render notes section of link id 25104: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25104: 0.0005800724029541 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/sccmecfinder\" id=\"link-24511\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SCCmecFinder<\/a>\n<!-- Time to render name section of link id 24511: 6.9141387939453E-6 --> \n<\/td>\n<td><p>SCCmecFinder identifies SCCmec elements in sequenced S. aureus isolates.<\/p>\n<!-- Time to render link large description section of link id 24511: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SCCmecFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24511: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24511: 0.00051999092102051 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/schmutzi\" id=\"link-23927\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">schmutzi<\/a>\n<!-- Time to render name section of link id 23927: 7.8678131103516E-6 --> \n<\/td>\n<td><p>Bayesian maximum a posteriori contamination estimate for ancient samples.<\/p>\n<!-- Time to render link large description section of link id 23927: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_schmutzi> How to use <\/a>\n<!-- Time to render notes section of link id 23927: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23927: 0.00051999092102051 --> \n<tr><td><a href=\"http:\/\/www.scipy.org\/\" id=\"link-23724\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">scipy<\/a>\n<!-- Time to render name section of link id 23724: 6.9141387939453E-6 --> \n<\/td>\n<td><p>SciPy (pronounced \"Sigh Pie\") is open-source software for mathematics, science, and engineering. The SciPy library depends on Numpy, which provides convenient and fast N-dimensional array manipulation.<\/p>\n<!-- Time to render link large description section of link id 23724: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> In Python modules<\/a>\n<!-- Time to render notes section of link id 23724: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23724: 0.00049996376037598 --> \n<tr><td><a href=\"https:\/\/github.com\/AdmiralenOla\/Scoary\" id=\"link-24512\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scoary<\/a>\n<!-- Time to render name section of link id 24512: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits.<\/p>\n<!-- Time to render link large description section of link id 24512: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Scoary> How to use <\/a>\n<!-- Time to render notes section of link id 24512: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24512: 0.0002589225769043 --> \n<tr><td><a href=\"https:\/\/scrm.github.io\/\" id=\"link-23883\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">scrm<\/a>\n<!-- Time to render name section of link id 23883: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A coalescent simulator for genome-scale sequences.<\/p>\n<!-- Time to render link large description section of link id 23883: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23883: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23883: 0.00026082992553711 --> \n<tr><td><a href=\"https:\/\/github.com\/mvollger\/SDA\" id=\"link-24052\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SDA<\/a>\n<!-- Time to render name section of link id 24052: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Segmental Duplication Assembler<\/p>\n<!-- Time to render link large description section of link id 24052: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24052: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24052: 0.00025701522827148 --> \n<tr><td><a href=\"https:\/\/github.com\/sex-det\/sdpop\" id=\"link-25703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SDpop<\/a>\n<!-- Time to render name section of link id 25703: 4.0531158447266E-6 --> \n<\/td>\n<td><p>SDpop infers sex-linkage from genotyping data of several individuals of both sexes, collected in panmictic populations.<\/p>\n<!-- Time to render link large description section of link id 25703: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SDpop> How to use <\/a>\n<!-- Time to render notes section of link id 25703: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25703: 0.0002589225769043 --> \n<tr><td><a href=\"https:\/\/github.com\/dpeerlab\/SEACells\" id=\"link-25223\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SEACells<\/a>\n<!-- Time to render name section of link id 25223: 3.0994415283203E-6 --> \n<\/td>\n<td><p dir=\"auto\"><strong>S<\/strong>ingle-c<strong>E<\/strong>ll <strong>A<\/strong>ggregation for High Resolution <strong>Cell S<\/strong>tates.<\/p>\r\n<p class=\"f4 my-3\">SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data.<\/p>\n<!-- Time to render link large description section of link id 25223: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SEACells> How to use <\/a>\n<!-- Time to render notes section of link id 25223: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25223: 0.00026702880859375 --> \n<tr><td><a href=\"https:\/\/github.com\/vpc-ccg\/sedef\" id=\"link-24028\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SEDEF<\/a>\n<!-- Time to render name section of link id 24028: 4.0531158447266E-6 --> \n<\/td>\n<td><p>SEDEF is a quick tool to find all segmental duplications in the genome.<\/p>\n<!-- Time to render link large description section of link id 24028: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24028: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24028: 0.00025796890258789 --> \n<tr><td><a href=\"https:\/\/www.bioinf.uni-leipzig.de\/Software\/segemehl\/\" id=\"link-24677\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">segemehl<\/a>\n<!-- Time to render name section of link id 24677: 3.814697265625E-6 --> \n<\/td>\n<td><p>segemehl is a software to map short sequencer reads to reference genomes. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).<\/p>\n<!-- Time to render link large description section of link id 24677: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24677: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24677: 0.0002598762512207 --> \n<tr><td><a href=\"https:\/\/github.com\/ay-lab\/selfish\" id=\"link-25259\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SELFISH<\/a>\n<!-- Time to render name section of link id 25259: 4.0531158447266E-6 --> \n<\/td>\n<td><p>SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.<\/p>\n<!-- Time to render link large description section of link id 25259: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SELFISH> How to use <\/a>\n<!-- Time to render notes section of link id 25259: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25259: 0.00026702880859375 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/simon.boitard\/snt\/\" id=\"link-25665\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SelNeTime<\/a>\n<!-- Time to render name section of link id 25665: 3.814697265625E-6 --> \n<\/td>\n<td><p>The selnetime python package implements methods for statistical analysis of genetic data collected for a same population at different times.<\/p>\n<!-- Time to render link large description section of link id 25665: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SelNeTime> How to use <\/a>\n<!-- Time to render notes section of link id 25665: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25665: 0.00025701522827148 --> \n<tr><td><a href=\"https:\/\/github.com\/szpiech\/selscan\" id=\"link-23725\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">selscan<\/a>\n<!-- Time to render name section of link id 23725: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A program to calculate EHH-based scans for positive selection in genomes.<\/p>\n<!-- Time to render link large description section of link id 23725: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_selscan> How to use <\/a>\n<!-- Time to render notes section of link id 23725: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23725: 0.0002589225769043 --> \n<tr><td><a href=\"https:\/\/seq-lang.org\/\" id=\"link-24514\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Seq<\/a>\n<!-- Time to render name section of link id 24514: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C\/C++.<\/p>\n<!-- Time to render link large description section of link id 24514: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Seq> How to use <\/a>\n<!-- Time to render notes section of link id 24514: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24514: 0.00021100044250488 --> \n<tr><td><a href=\"http:\/\/tree.bio.ed.ac.uk\/software\/seqgen\/\" id=\"link-23814\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Seq-Gen<\/a>\n<!-- Time to render name section of link id 23814: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.<\/p>\n<!-- Time to render link large description section of link id 23814: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23814: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23814: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/www.seqan.de\/\" id=\"link-24074\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SeqAn<\/a>\n<!-- Time to render name section of link id 24074: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.<\/p>\n<!-- Time to render link large description section of link id 24074: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SeqAn> How to use <\/a>\n<!-- Time to render notes section of link id 24074: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24074: 0.00016188621520996 --> \n<tr><td><a href=\"ftp:\/\/occams.dfci.harvard.edu\/pub\/bio\/tgi\/software\/seqclean\/\" id=\"link-23896\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqclean<\/a>\n<!-- Time to render name section of link id 23896: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SeqClean is a tool for validation and trimming of DNA sequences from a flat file database (FASTA format).<\/p>\n<!-- Time to render link large description section of link id 23896: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqclean> How to use <\/a>\n<!-- Time to render notes section of link id 23896: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23896: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/clwgg\/seqfilter\" id=\"link-23964\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqfilter<\/a>\n<!-- Time to render name section of link id 23964: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Filter fasta\/fastq(.gz) files by ID and\/or sequence length<\/p>\n<!-- Time to render link large description section of link id 23964: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23964: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23964: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/telatin\/seqfu2\" id=\"link-25022\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SeqFu<\/a>\n<!-- Time to render name section of link id 25022: 3.0994415283203E-6 --> \n<\/td>\n<td><p dir=\"auto\">A general-purpose program to manipulate and parse information from FASTA\/FASTQ files, supporting gzipped input files. Includes functions to\u00a0<em>interleave<\/em>\u00a0and\u00a0<em>de-interleave<\/em>\u00a0FASTQ files, to\u00a0<em>rename<\/em>\u00a0sequences and to\u00a0<em>count<\/em>\u00a0and print\u00a0<em>statistics<\/em>\u00a0on sequence lengths.<\/p>\n<!-- Time to render link large description section of link id 25022: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SeqFu> How to use <\/a>\n<!-- Time to render notes section of link id 25022: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25022: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/bioinf.shenwei.me\/seqkit\/\" id=\"link-24020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SeqKit<\/a>\n<!-- Time to render name section of link id 24020: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A cross-platform and ultrafast toolkit for FASTA\/Q file manipulation. Common manipulations of FASTA\/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling.<\/p>\n<!-- Time to render link large description section of link id 24020: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SeqKit> How to use <\/a>\n<!-- Time to render notes section of link id 24020: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24020: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/seqtk\" id=\"link-23902\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Seqtk<\/a>\n<!-- Time to render name section of link id 23902: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Toolkit for processing sequences in FASTA\/Q formats<\/p>\n<!-- Time to render link large description section of link id 23902: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Seqtk> How to use <\/a>\n<!-- Time to render notes section of link id 23902: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23902: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/stschiff\/sequenceTools\" id=\"link-24078\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SequenceTools<\/a>\n<!-- Time to render name section of link id 24078: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Tools for population genetics on sequencing datas<\/p>\n<!-- Time to render link large description section of link id 24078: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SequenceTools> How to use <\/a>\n<!-- Time to render notes section of link id 24078: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24078: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/seqwish\" id=\"link-24515\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqwish<\/a>\n<!-- Time to render name section of link id 24515: 1.9073486328125E-6 --> \n<\/td>\n<td><p>seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments.<\/p>\n<!-- Time to render link large description section of link id 24515: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqwish> How to use <\/a>\n<!-- Time to render notes section of link id 24515: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24515: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/jts\/sga\" id=\"link-23726\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SGA<\/a>\n<!-- Time to render name section of link id 23726: 5.9604644775391E-6 --> \n<\/td>\n<td><p>SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.<\/p>\n<!-- Time to render link large description section of link id 23726: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23726: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23726: 0.00050687789916992 --> \n<tr><td><a href=\"https:\/\/www.appliedbioinformatics.com.au\/Edwards\/index.php\/SGSGeneLoss\" id=\"link-24516\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SGSGeneLoss<\/a>\n<!-- Time to render name section of link id 24516: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Gene presence\/absence variation discovery.<\/p>\n<!-- Time to render link large description section of link id 24516: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24516: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24516: 0.00051999092102051 --> \n<tr><td><a href=\"https:\/\/mathgen.stats.ox.ac.uk\/genetics_software\/shapeit\/shapeit.html#home\" id=\"link-23771\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SHAPEIT<\/a>\n<!-- Time to render name section of link id 23771: 6.9141387939453E-6 --> \n<\/td>\n<td><p>SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23771: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SHAPEIT> How to use <\/a>\n<!-- Time to render notes section of link id 23771: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23771: 0.00052094459533691 --> \n<tr><td><a href=\"https:\/\/github.com\/paoloshasta\/shasta\" id=\"link-24118\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Shasta<\/a>\n<!-- Time to render name section of link id 24118: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.<\/p>\n<!-- Time to render link large description section of link id 24118: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Shasta> How to use <\/a>\n<!-- Time to render notes section of link id 24118: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24118: 0.00049495697021484 --> \n<tr><td><a href=\"https:\/\/github.com\/bootphon\/shennong\" id=\"link-26030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Shennong<\/a>\n<!-- Time to render name section of link id 26030: 8.1062316894531E-6 --> \n<\/td>\n<td><p>A Python toolbox for speech features extraction.<\/p>\n<!-- Time to render link large description section of link id 26030: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Shennong> How to use <\/a>\n<!-- Time to render notes section of link id 26030: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26030: 0.00050115585327148 --> \n<tr><td><a href=\"https:\/\/github.com\/phylo42\/sherpas\" id=\"link-25986\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SHERPAS<\/a>\n<!-- Time to render name section of link id 25986: 7.1525573730469E-6 --> \n<\/td>\n<td><p>A new, alignment-free genome recombination detection tool exploiting the idea of phylo-kmers (originally developed in RAPPAS, Linard et al. 2019) to accelerate the process by several orders of magnitude while keeping comparable accuracy.<\/p>\n<!-- Time to render link large description section of link id 25986: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SHERPAS> How to use <\/a>\n<!-- Time to render notes section of link id 25986: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25986: 0.00050997734069824 --> \n<tr><td><a href=\"https:\/\/github.com\/ChrisHIV\/shiver\" id=\"link-24670\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">shiver<\/a>\n<!-- Time to render name section of link id 24670: 6.9141387939453E-6 --> \n<\/td>\n<td><p>shiver is a tool for mapping paired-end short reads to a custom reference sequence constructed using do novo assembled contigs, in order to minimise the biased loss of information that occurs from mapping to a reference that differs from the sample.<\/p>\n<!-- Time to render link large description section of link id 24670: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24670: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24670: 0.0005190372467041 --> \n<tr><td><a href=\"https:\/\/github.com\/MikeAxtell\/ShortStack\" id=\"link-23727\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ShortStack<\/a>\n<!-- Time to render name section of link id 23727: 6.9141387939453E-6 --> \n<\/td>\n<td><p>ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.<\/p>\n<!-- Time to render link large description section of link id 23727: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ShortStack> How to use <\/a>\n<!-- Time to render notes section of link id 23727: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23727: 0.00052285194396973 --> \n<tr><td><a href=\"http:\/\/compbio.cs.toronto.edu\/shrimp\/\" id=\"link-24088\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SHRiMP<\/a>\n<!-- Time to render name section of link id 24088: 2.8610229492188E-6 --> \n<\/td>\n<td><p>SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.<\/p>\n<!-- Time to render link large description section of link id 24088: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24088: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24088: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/medvedevgroup\/SibeliaZ\" id=\"link-24517\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SibeliaZ<\/a>\n<!-- Time to render name section of link id 24517: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SibeliaZ is a whole-genome alignment and locally-coliinear blocks construction pipeline. The blocks coordinates are output in GFF format and the alignment is in MAF.<\/p>\n<!-- Time to render link large description section of link id 24517: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SibeliaZ> How to use <\/a>\n<!-- Time to render notes section of link id 24517: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24517: 0.00022006034851074 --> \n<tr><td><a href=\"https:\/\/github.com\/zanglab\/SICER2\" id=\"link-24518\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SICER2<\/a>\n<!-- Time to render name section of link id 24518: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Redesigned and improved version of the original ChIP-seq broad peak calling tool SICER.<\/p>\n<!-- Time to render link large description section of link id 24518: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SICER2> How t o use <\/a>\n<!-- Time to render notes section of link id 24518: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24518: 0.00022983551025391 --> \n<tr><td><a href=\"https:\/\/github.com\/najoshi\/sickle\" id=\"link-23728\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sickle<\/a>\n<!-- Time to render name section of link id 23728: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.<\/p>\n<!-- Time to render link large description section of link id 23728: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sickle> How to use <\/a>\n<!-- Time to render notes section of link id 23728: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23728: 0.00021791458129883 --> \n<tr><td><a href=\"https:\/\/github.com\/rvaser\/sift4g\" id=\"link-24723\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SIFT4G<\/a>\n<!-- Time to render name section of link id 24723: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Sorting Intolerant From Tolerant For Genomes.<\/p>\n<!-- Time to render link large description section of link id 24723: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SIFT4G> How to use <\/a>\n<!-- Time to render notes section of link id 24723: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24723: 0.00021696090698242 --> \n<tr><td><a href=\"https:\/\/github.com\/pauline-ng\/SIFT4G_Annotator\" id=\"link-24724\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SIFT4G_Annotator<\/a>\n<!-- Time to render name section of link id 24724: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Annotating VCF files using the SIFT4G databases.<\/p>\n<!-- Time to render link large description section of link id 24724: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24724: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24724: 0.00021696090698242 --> \n<tr><td><a href=\"http:\/\/www.cbs.dtu.dk\/services\/SignalP\/\" id=\"link-23729\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SignalP<\/a>\n<!-- Time to render name section of link id 23729: 3.0994415283203E-6 --> \n<\/td>\n<td><div>SignalP 4.0 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.<\/div>\n<!-- Time to render link large description section of link id 23729: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SignalP> How to use <\/a>\n<!-- Time to render notes section of link id 23729: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23729: 0.00022006034851074 --> \n<tr><td><a href=\"http:\/\/lbbe.univ-lyon1.fr\/Overview.html?lang=fr\" id=\"link-23914\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Silix<\/a>\n<!-- Time to render name section of link id 23914: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.<\/p>\n<!-- Time to render link large description section of link id 23914: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SiLiX> How to use <\/a>\n<!-- Time to render notes section of link id 23914: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23914: 0.0002288818359375 --> \n<tr><td><a href=\"https:\/\/gatb.inria.fr\/software\/simka\/\" id=\"link-24676\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Simka<\/a>\n<!-- Time to render name section of link id 24676: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.<\/p>\n<!-- Time to render link large description section of link id 24676: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Simka> How to use <\/a>\n<!-- Time to render notes section of link id 24676: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24676: 0.00022101402282715 --> \n<tr><td><a href=\"http:\/\/simupop.sourceforge.net\/Main\/HomePage\" id=\"link-23730\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">simuPOP<\/a>\n<!-- Time to render name section of link id 23730: 3.0994415283203E-6 --> \n<\/td>\n<td><p>simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.<\/p>\n<!-- Time to render link large description section of link id 23730: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23730: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23730: 0.00021791458129883 --> \n<tr><td><a href=\"https:\/\/github.com\/wwood\/singlem\" id=\"link-24519\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">singlem<\/a>\n<!-- Time to render name section of link id 24519: 3.814697265625E-6 --> \n<\/td>\n<td><p>SingleM is a tool to find the abundances of discrete operational taxonomic units (OTUs) directly from shotgun metagenome data, without heavy reliance on reference sequence databases. It is able to differentiate closely related species even if those species are from lineages new to science.<\/p>\n<!-- Time to render link large description section of link id 24519: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24519: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24519: 0.00021815299987793 --> \n<tr><td><a href=\"https:\/\/github.com\/sylabs\/singularity\" id=\"link-24002\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Singularity<\/a>\n<!-- Time to render name section of link id 24002: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Singularity enables users to have full control of their environment. Singularity containers can be used to package entire scientific workflows, software and libraries, and even data.<\/p>\n<!-- Time to render link large description section of link id 24002: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_singularity> How to use <\/a>\n<!-- Time to render notes section of link id 24002: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24002: 0.00022101402282715 --> \n<tr><td><a href=\"http:\/\/pachterlab.github.io\/sleuth\/\" id=\"link-23777\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sleuth<\/a>\n<!-- Time to render name section of link id 23777: 2.8610229492188E-6 --> \n<\/td>\n<td><p>sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.<\/p>\n<!-- Time to render link large description section of link id 23777: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23777: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23777: 0.0002281665802002 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/a\/ucr.edu\/slicembler\/home\" id=\"link-24520\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLICEMBLER<\/a>\n<!-- Time to render name section of link id 24520: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SLICEMBLER is a meta-assembler designed for ultra-deep sequencing data\/<\/p>\n<!-- Time to render link large description section of link id 24520: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24520: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24520: 0.00017213821411133 --> \n<tr><td><a href=\"https:\/\/messerlab.org\/slim\/\" id=\"link-23831\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLiM<\/a>\n<!-- Time to render name section of link id 23831: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.<\/p>\n<!-- Time to render link large description section of link id 23831: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SLiM> How to use <\/a>\n<!-- Time to render notes section of link id 23831: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23831: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/www.ebi.ac.uk\/research\/goldman\/software\/slr\/\" id=\"link-24090\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLR<\/a>\n<!-- Time to render name section of link id 24090: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SLR is a program to detect sites in coding DNA that are unusually conserved and\/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree.<\/p>\n<!-- Time to render link large description section of link id 24090: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SLR> How to use <\/a>\n<!-- Time to render notes section of link id 24090: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24090: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/SLR-superscaffolder\" id=\"link-24521\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLR-superscaffolder<\/a>\n<!-- Time to render name section of link id 24521: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is a scaffold assembler designed for stLFR reads. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds.<\/p>\n<!-- Time to render link large description section of link id 24521: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24521: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24521: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/www.sanger.ac.uk\/science\/tools\/smalt-0\" id=\"link-24031\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SMALT<\/a>\n<!-- Time to render name section of link id 24031: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SMALT aligns DNA sequencing reads with a reference genome.<\/p>\r\n<p>Reads from a wide range of sequencing platforms can be processed, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads are supported. There is no support for SOLiD reads.<\/p>\n<!-- Time to render link large description section of link id 24031: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24031: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24031: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/ruanjue\/smartdenovo\" id=\"link-23845\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">smartdenovo<\/a>\n<!-- Time to render name section of link id 23845: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.<\/p>\n<!-- Time to render link large description section of link id 23845: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_smartdenovo> How to use <\/a>\n<!-- Time to render notes section of link id 23845: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23845: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenmethods\/smcpp\" id=\"link-24522\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SMC++<\/a>\n<!-- Time to render name section of link id 24522: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SMC++ is a program for estimating the size history of populations from whole genome sequence data.<\/p>\n<!-- Time to render link large description section of link id 24522: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SMC++> How to use <\/a>\n<!-- Time to render notes section of link id 24522: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24522: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/www.pacb.com\/support\/software-downloads\/\" id=\"link-23904\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SMRTLink<\/a>\n<!-- Time to render name section of link id 23904: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SMRT Link is the web-based end-to-end workflow manager for the Sequel\u2122 System. (installed in mode command line on our cluster)<\/p>\n<!-- Time to render link large description section of link id 23904: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SMRTLink> How to use <\/a>\n<!-- Time to render notes section of link id 23904: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23904: 0.0001838207244873 --> \n<tr><td><a href=\"https:\/\/github.com\/tbenavi1\/smudgeplot\" id=\"link-24073\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Smudgeplots<\/a>\n<!-- Time to render name section of link id 24073: 1.2874603271484E-5 --> \n<\/td>\n<td><p>Inference of ploidy and heterozygosity structure using whole genome sequencing data. This tool extracts heterozygous kmer pairs from kmer dump files (from jellyfish or KMC) and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA \/ (CovA + CovB)). Smudgeplots are computed from raw\/trimmed reads and show the haplotype structure using heterozygous kmer pairs.<\/p>\n<!-- Time to render link large description section of link id 24073: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_smudgeplot> How to use <\/a>\n<!-- Time to render notes section of link id 24073: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24073: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/snakemake\/\" id=\"link-23807\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Snakemake<\/a>\n<!-- Time to render name section of link id 23807: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style.<\/p>\n<!-- Time to render link large description section of link id 23807: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Snakemake> How to use <\/a>\n<!-- Time to render notes section of link id 23807: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23807: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/maxplanck-ie\/snakepipes\" id=\"link-24523\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snakePipes<\/a>\n<!-- Time to render name section of link id 24523: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Customizable workflows based on snakemake and python for the analysis of NGS data.<\/p>\n<!-- Time to render link large description section of link id 24523: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24523: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24523: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/KorfLab\/SNAP\" id=\"link-23824\" class=\"track_this_link \" rel=\"noopener noreferrer\">SNAP<\/a>\n<!-- Time to render name section of link id 23824: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Gene prediction tool<\/p>\n<!-- Time to render link large description section of link id 23824: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNAP> How to use <\/a>\n<!-- Time to render notes section of link id 23824: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23824: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/snape-pooled\/\" id=\"link-24089\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snape-pooled<\/a>\n<!-- Time to render name section of link id 24089: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.<\/p>\n<!-- Time to render link large description section of link id 24089: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24089: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24089: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/fritzsedlazeck\/Sniffles\" id=\"link-24524\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sniffles<\/a>\n<!-- Time to render name section of link id 24524: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.<\/p>\n<!-- Time to render link large description section of link id 24524: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sniffles> How to use <\/a>\n<!-- Time to render notes section of link id 24524: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24524: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/tseemann\/snippy\" id=\"link-24075\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Snippy<\/a>\n<!-- Time to render name section of link id 24075: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Rapid haploid variant calling and core genome alignment. Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions\/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree).<\/p>\n<!-- Time to render link large description section of link id 24075: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Snippy> How to use <\/a>\n<!-- Time to render notes section of link id 24075: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24075: 0.0001981258392334 --> \n<tr><td><a href=\"http:\/\/membres-timc.imag.fr\/Olivier.Francois\/snmf\/index.htm\" id=\"link-23998\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sNMF<\/a>\n<!-- Time to render name section of link id 23998: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics.<\/p>\n<!-- Time to render link large description section of link id 23998: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23998: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23998: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/snoGPS\/\" id=\"link-25293\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snoGPS<\/a>\n<!-- Time to render name section of link id 25293: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Search for H\/ACA snoRNA genes in a genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 25293: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_snoGPS> How to use <\/a>\n<!-- Time to render notes section of link id 25293: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25293: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-leipzig.de\/Software\/snoReport\/\" id=\"link-23731\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SnoReport<\/a>\n<!-- Time to render name section of link id 23731: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Computational identification of snoRNAs with unknown targets.<br \/>\r\nDetecting novel or orphan snoRNAs in RNA sequence data using sequence and structure information only without relying on target information<\/p>\n<!-- Time to render link large description section of link id 23731: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23731: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23731: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/snoscan\" id=\"link-25262\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Snoscan<\/a>\n<!-- Time to render name section of link id 25262: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Search for C\/D box methylation guide snoRNA genes in a genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 25262: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Snoscan> How to use <\/a>\n<!-- Time to render notes section of link id 25262: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25262: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-pathogens\/snp-sites\" id=\"link-24861\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNP-sites<\/a>\n<!-- Time to render name section of link id 24861: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Rapidly extracts SNPs from a multi-FASTA alignment.<\/p>\n<!-- Time to render link large description section of link id 24861: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNP-sites> How to use <\/a>\n<!-- Time to render notes section of link id 24861: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24861: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/harvardinformatics\/snpArcher\" id=\"link-25580\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snpArcher<\/a>\n<!-- Time to render name section of link id 25580: 1.9073486328125E-6 --> \n<\/td>\n<td><p>snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakemake workflow management system, for dataset acquisition, variant calling, quality control, and downstream analysis.<\/p>\n<!-- Time to render link large description section of link id 25580: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_snpArcher> How to use <\/a>\n<!-- Time to render notes section of link id 25580: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25580: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/pcingola.github.io\/SnpEff\/\" id=\"link-23732\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SnpEff<\/a>\n<!-- Time to render name section of link id 23732: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SnpEff is a variant annotation and effect prediction tool. ttttIt annotates and predicts the effects of variants on genes (such as amino acid changes)<\/p>\n<!-- Time to render link large description section of link id 23732: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SnpEff> How to use <\/a>\n<!-- Time to render notes section of link id 23732: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23732: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/biocore-ntnu\/snpflip\" id=\"link-25984\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snpflip<\/a>\n<!-- Time to render name section of link id 25984: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Report reverse and ambiguous strand SNPs in GWAS data.<\/p>\n<!-- Time to render link large description section of link id 25984: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_snpflip> How to use <\/a>\n<!-- Time to render notes section of link id 25984: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25984: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/chasewnelson\/SNPGenie\" id=\"link-24525\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPGenie<\/a>\n<!-- Time to render name section of link id 24525: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SNPGenie is a collection of Perl scripts for estimating \u03c0N\/\u03c0S, dN\/dS, and gene diversity from next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data.<\/p>\n<!-- Time to render link large description section of link id 24525: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24525: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24525: 0.00019097328186035 --> \n<tr><td><a href=\"http:\/\/chibba.pgml.uga.edu\/snphylo\" id=\"link-23795\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPhylo<\/a>\n<!-- Time to render name section of link id 23795: 1.9073486328125E-6 --> \n<\/td>\n<td><p>a pipeline to generate a phylogenetic tree from huge SNP data<\/p>\n<!-- Time to render link large description section of link id 23795: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNPhylo> How to use <\/a>\n<!-- Time to render notes section of link id 23795: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23795: 0.00018215179443359 --> \n<tr><td><a href=\"https:\/\/github.com\/FelixKrueger\/SNPsplit\" id=\"link-25013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPsplit<\/a>\n<!-- Time to render name section of link id 25013: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SNPsplit is an allele-specific alignment sorter which is designed to read alignment files in SAM\/BAM format and determine the allelic origin of reads that cover known SNP positions.<\/p>\n<!-- Time to render link large description section of link id 25013: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNPsplit> How to use <\/a>\n<!-- Time to render notes section of link id 25013: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25013: 0.00017213821411133 --> \n<tr><td><a href=\"https:\/\/github.com\/gigascience\/bgi-soap2\/tree\/master\/tools\/soap.coverage\/2.7.7\" id=\"link-24526\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">soap.coverage<\/a>\n<!-- Time to render name section of link id 24526: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Can calculate sequencing coverage or physical coverage as well as duplication rate and details of specific block for each segments and whole genome by using SOAP, Blat, Blast, BlastZ, mummer and MAQ aligement results with multi-thread. Gzip file supported.<\/p>\n<!-- Time to render link large description section of link id 24526: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24526: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24526: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/soap.genomics.org.cn\/soapdenovo.html\" id=\"link-23733\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SOAPdenovo<\/a>\n<!-- Time to render name section of link id 23733: 3.0994415283203E-6 --> \n<\/td>\n<td><div class=\"title\">ttSOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. <b><br \/>\r\n<\/b><\/div>\n<!-- Time to render link large description section of link id 23733: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23733: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23733: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/aquaskyline\/SOAPdenovo-Trans\" id=\"link-24527\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SOAPdenovo-Trans<\/a>\n<!-- Time to render name section of link id 24527: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.<\/p>\n<!-- Time to render link large description section of link id 24527: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24527: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24527: 0.00019598007202148 --> \n<tr><td><a href=\"https:\/\/github.com\/calkan\/sonic\" id=\"link-24853\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sonic<\/a>\n<!-- Time to render name section of link id 24853: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Some Organism's Nucleotide Information Container.<\/p>\n<!-- Time to render link large description section of link id 24853: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24853: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24853: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/FePhyFoFum\/sortadate\" id=\"link-23958\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SortaDate<\/a>\n<!-- Time to render name section of link id 23958: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scripts that you can use at different stages to attempt to find more clock-like genes. Generally, you would use these for dating analyses with another package<\/p>\n<!-- Time to render link large description section of link id 23958: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23958: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23958: 0.00019192695617676 --> \n<tr><td><a href=\"http:\/\/bioinfo.lifl.fr\/RNA\/sortmerna\/index.php\" id=\"link-23734\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SortMeRNA<\/a>\n<!-- Time to render name section of link id 23734: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity<\/p>\n<!-- Time to render link large description section of link id 23734: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SortMeRNA> How to use <\/a>\n<!-- Time to render notes section of link id 23734: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23734: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/wheaton5\/souporcell\" id=\"link-25263\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">souporcell<\/a>\n<!-- Time to render name section of link id 25263: 3.0994415283203E-6 --> \n<\/td>\n<td><p>souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.<\/p>\n<!-- Time to render link large description section of link id 25263: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_souporcell> How to use <\/a>\n<!-- Time to render notes section of link id 25263: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25263: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/sourmash.readthedocs.io\/en\/latest\/\" id=\"link-24529\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sourmash<\/a>\n<!-- Time to render name section of link id 24529: 1.9073486328125E-6 --> \n<\/td>\n<td><p>sourmash is a command-line tool and Python library for computing hash sketches from DNA sequences, comparing them to each other, and plotting the results.<\/p>\n<!-- Time to render link large description section of link id 24529: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sourmash> How to use <\/a>\n<!-- Time to render notes section of link id 24529: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24529: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/spatial-gene-expression\/software\/pipelines\/latest\/what-is-space-ranger\" id=\"link-24530\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpaceRanger<\/a>\n<!-- Time to render name section of link id 24530: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield and fluorescence microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.<\/p>\n<!-- Time to render link large description section of link id 24530: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SpaceRanger> How to use <\/a>\n<!-- Time to render notes section of link id 24530: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24530: 0.00016379356384277 --> \n<tr><td><a href=\"http:\/\/cab.spbu.ru\/software\/spades\/\" id=\"link-23735\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SPAdes<\/a>\n<!-- Time to render name section of link id 23735: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SPAdes \uff96 St. Petersburg genome assembler \uff96 is intended for both standard isolates and single-cell MDA bacteria assemblies.<\/p>\n<!-- Time to render link large description section of link id 23735: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SPAdes> How to use <\/a>\n<!-- Time to render notes section of link id 23735: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23735: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/ogotoh\/spaln\" id=\"link-24531\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Spaln<\/a>\n<!-- Time to render name section of link id 24531: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.<\/p>\n<!-- Time to render link large description section of link id 24531: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Spaln> How to use <\/a>\n<!-- Time to render notes section of link id 24531: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24531: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/HCGB-IGTP\/spaTyper\" id=\"link-24532\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spaTyper<\/a>\n<!-- Time to render name section of link id 24532: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Computational method for finding spa types. Staphylococcus aureus\u00a0is a major human pathogen causing skin and tissue infections, pneumonia, septicemia, and device-associated infections. The emergence of strains resistant to methicillin (MRSA) and other antibacterial agents has become a major concern, especially in the hospital environment, because of the high mortality of the infections caused by these strains. Single locus DNA-sequencing of the repeat region of the\u00a0Staphylococcus\u00a0protein A gene (spa) can be used for reliable, accurate and discriminatory typing of MRSA. Repeats are assigned a numerical code and the spa-type is deduced from the order of specific repeats. However, spa-typing was hampered in the past by the lack of a consensus on assignments of new spa-repeats and -types.<\/p>\n<!-- Time to render link large description section of link id 24532: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24532: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24532: 0.00016212463378906 --> \n<tr><td><a href=\"https:\/\/github.com\/maplesond\/spectre\" id=\"link-24069\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SPECTRE<\/a>\n<!-- Time to render name section of link id 24069: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A collection of Phylogenetics tools for creating and manipulating networks and trees.<\/p>\n<!-- Time to render link large description section of link id 24069: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24069: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24069: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/hall-lab\/speedseq\" id=\"link-24128\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpeedSeq<\/a>\n<!-- Time to render name section of link id 24128: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A flexible framework for rapid genome analysis and interpretation.<\/p>\n<!-- Time to render link large description section of link id 24128: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24128: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24128: 0.00016999244689941 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/spliced_bam2gff\" id=\"link-24605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spliced_bam2gff<\/a>\n<!-- Time to render name section of link id 24605: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool to convert spliced BAM alignments into GFF2 format.<\/p>\n<!-- Time to render link large description section of link id 24605: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24605: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24605: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/splicegrapher\/\" id=\"link-24533\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpliceGrapher<\/a>\n<!-- Time to render name section of link id 24533: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SpliceGrapher predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene's exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.<\/p>\n<!-- Time to render link large description section of link id 24533: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24533: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24533: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/flemingtonlab\/SpliceTools\" id=\"link-25326\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpliceTools<\/a>\n<!-- Time to render name section of link id 25326: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing, Nucleic Acids Research, 2023.<\/p>\n<!-- Time to render link large description section of link id 25326: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SpliceTools> How to use <\/a>\n<!-- Time to render notes section of link id 25326: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25326: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/rvaser\/spoa\" id=\"link-24534\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Spoa<\/a>\n<!-- Time to render name section of link id 24534: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A multiple sequence alignment tool\/library that implements the POA (partial order alignement) algorithm using SIMD.<\/p>\n<!-- Time to render link large description section of link id 24534: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24534: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24534: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/sprai-doc.readthedocs.io\/en\/latest\/\" id=\"link-24535\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sprai<\/a>\n<!-- Time to render name section of link id 24535: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Sprai (single-pass read accuracy improver) is a tool to correct sequencing errors in single-pass reads for de novo assembly.<\/p>\n<!-- Time to render link large description section of link id 24535: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24535: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24535: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/marekborowiec\/spruceup\" id=\"link-24536\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spruceup<\/a>\n<!-- Time to render name section of link id 24536: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tools to discover, visualize, and remove outlier sequences in large multiple sequence alignments.<\/p>\n<!-- Time to render link large description section of link id 24536: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24536: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24536: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/splatlab\/squeakr\" id=\"link-24538\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">squeakr<\/a>\n<!-- Time to render name section of link id 24538: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Squeakr is a k-mer-counting and multiset-representation system using the recently-introduced counting quotient filter (CQF) Pandey et al. (2017), a feature-rich approximate membership query (AMQ) data structure.<\/p>\n<!-- Time to render link large description section of link id 24538: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24538: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24538: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/software\/squid\/\" id=\"link-23906\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">squid<\/a>\n<!-- Time to render name section of link id 23906: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A C library that is bundled with much of the above software. C function library for sequence analysis.<\/p>\n<!-- Time to render link large description section of link id 23906: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23906: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23906: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/Psy-Fer\/SquiggleKit\" id=\"link-24127\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SquiggleKit<\/a>\n<!-- Time to render name section of link id 24127: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A toolkit for manipulating nanopore signal data.<\/p>\n<!-- Time to render link large description section of link id 24127: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24127: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24127: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/wyang17\/SQuIRE\" id=\"link-24539\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SQuIRE<\/a>\n<!-- Time to render name section of link id 24539: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SQuIRE reveals locus-specific regulation of interspersed repeat expression, Nucleic Acids Research<\/p>\n<!-- Time to render link large description section of link id 24539: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SQuIRE> How to use <\/a>\n<!-- Time to render notes section of link id 24539: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24539: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/BrendelGroup\/SRAssembler\" id=\"link-24540\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SRAsembler<\/a>\n<!-- Time to render name section of link id 24540: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SRAssembler (Selective Recursive local Assembler) is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologous to a query DNA or protein sequence.<\/p>\n<!-- Time to render link large description section of link id 24540: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24540: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24540: 0.00017285346984863 --> \n<tr><td><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Traces\/sra\/sra.cgi?view=doc\" id=\"link-23736\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SRAToolkit<\/a>\n<!-- Time to render name section of link id 23736: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Toolkit to query Short Reads Archive at NCBI<\/p>\n<!-- Time to render link large description section of link id 23736: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SRA-Toolkit> How to use <\/a>\n<!-- Time to render notes section of link id 23736: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23736: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/mzytnicki\/srnaMapper\" id=\"link-24541\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">srnaMapper<\/a>\n<!-- Time to render name section of link id 24541: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This tool maps reads produced by sRNA-Seq to a genome.<\/p>\n<!-- Time to render link large description section of link id 24541: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24541: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24541: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/lihan97\/sslHiC\" id=\"link-25348\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sslHiC<\/a>\n<!-- Time to render name section of link id 25348: 2.1457672119141E-6 --> \n<\/td>\n<td><p>sslHiC is a computational framework for comparative analyses of Hi-C data, including reproducibility measurement and differential chromatin interaction (DCI) detection.<\/p>\n<!-- Time to render link large description section of link id 25348: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sslHiC> How to use <\/a>\n<!-- Time to render notes section of link id 25348: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25348: 0.00018095970153809 --> \n<tr><td><a href=\"http:\/\/www.baseclear.com\/lab-products\/bioinformatics-tools\/sspace-standard\/\" id=\"link-23737\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SSPACE<\/a>\n<!-- Time to render name section of link id 23737: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS\u00a0 paired-read data.<\/p>\n<!-- Time to render link large description section of link id 23737: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23737: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23737: 0.00018191337585449 --> \n<tr><td><a href=\"http:\/\/www.baseclear.com\/genomics\/bioinformatics\/basetools\/SSPACE_longread\" id=\"link-23738\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SSPACE-LongRead<\/a>\n<!-- Time to render name section of link id 23738: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads).<\/p>\n<!-- Time to render link large description section of link id 23738: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23738: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23738: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/software\/ssu-align\/\" id=\"link-24542\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SSU-ALIGN<\/a>\n<!-- Time to render name section of link id 24542: 3.0994415283203E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 24542: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24542: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24542: 0.00022006034851074 --> \n<tr><td><a href=\"http:\/\/catchenlab.life.illinois.edu\/stacks\/\" id=\"link-23739\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Stacks<\/a>\n<!-- Time to render name section of link id 23739: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Stacks is a software suite for analysing RAD Sequencing data by Julian Catchen at the University of Oregon. It will process raw Illumina RAD data or RAD data aligned to a reference genome, and produce genotypes that can be viewed and filtered via a web interface.<\/p>\n<!-- Time to render link large description section of link id 23739: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Stacks> How to use <\/a>\n<!-- Time to render notes section of link id 23739: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23739: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/jpopgen\/stairway-plot\" id=\"link-24032\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">stairway_plot<\/a>\n<!-- Time to render name section of link id 24032: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data. It does not need a pre-defined population model and can be applied to hundreds of unphased sequences.<\/p>\n<!-- Time to render link large description section of link id 24032: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_stairway_plot> How to use <\/a>\n<!-- Time to render notes section of link id 24032: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24032: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/alexdobin\/STAR\" id=\"link-23912\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STAR<\/a>\n<!-- Time to render name section of link id 23912: 2.8610229492188E-6 --> \n<\/td>\n<td><p><span class=\"col-11 text-gray-dark mr-2\">RNA-seq aligner<\/span><\/p>\n<!-- Time to render link large description section of link id 23912: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_STAR> How to use <\/a>\n<!-- Time to render notes section of link id 23912: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23912: 0.00018978118896484 --> \n<tr><td><a href=\"https:\/\/github.com\/STAR-Fusion\/STAR-Fusion\" id=\"link-23740\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STAR-Fusion<\/a>\n<!-- Time to render name section of link id 23740: 2.8610229492188E-6 --> \n<\/td>\n<td><p>STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set (using a GTF file, ideally the same annotation file used during the STAR genome index building process during the intial STAR setup).<\/p>\n<!-- Time to render link large description section of link id 23740: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_STAR-Fusion> How to use <\/a>\n<!-- Time to render notes section of link id 23740: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23740: 0.00020909309387207 --> \n<tr><td><a href=\"https:\/\/github.com\/rwdavies\/STITCH\" id=\"link-24543\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STITCH<\/a>\n<!-- Time to render name section of link id 24543: 2.8610229492188E-6 --> \n<\/td>\n<td><p>STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation.<\/p>\n<!-- Time to render link large description section of link id 24543: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24543: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24543: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/strelka\" id=\"link-23984\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Strelka<\/a>\n<!-- Time to render name section of link id 23984: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor\/normal sample pairs.<\/p>\n<!-- Time to render link large description section of link id 23984: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Strelka> How to use <\/a>\n<!-- Time to render notes section of link id 23984: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23984: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/stringtie\" id=\"link-23741\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">StringTie<\/a>\n<!-- Time to render name section of link id 23741: 2.8610229492188E-6 --> \n<\/td>\n<td><p><b>StringTie<\/b> is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional <i>de novo<\/i> assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.<\/p>\n<!-- Time to render link large description section of link id 23741: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_StringTie> How to use <\/a>\n<!-- Time to render notes section of link id 23741: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23741: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/ksahlin\/StrobeAlign\" id=\"link-24544\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">StrobeAlign<\/a>\n<!-- Time to render name section of link id 24544: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Aligns short reads using dynamic seed size with strobemers.<\/p>\n<!-- Time to render link large description section of link id 24544: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24544: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24544: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/web.stanford.edu\/group\/pritchardlab\/home.html\" id=\"link-23742\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Structure<\/a>\n<!-- Time to render name section of link id 23742: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The program <b>structure<\/b> is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.<\/p>\n<!-- Time to render link large description section of link id 23742: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Structure> How to use <\/a>\n<!-- Time to render notes section of link id 23742: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23742: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/marcpaga\/sturgeon\" id=\"link-25424\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sturgeon<\/a>\n<!-- Time to render name section of link id 25424: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Sturgeon is a CNS neural network classifier for tumour classification<\/p>\n<!-- Time to render link large description section of link id 25424: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sturgeon> How to use <\/a>\n<!-- Time to render notes section of link id 25424: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25424: 0.00021195411682129 --> \n<tr><td><a href=\"http:\/\/bioinf.wehi.edu.au\/subread-package\/\" id=\"link-23743\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Subread<\/a>\n<!-- Time to render name section of link id 23743: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A tool kit for processing next-gen sequencing data<\/p>\n<!-- Time to render link large description section of link id 23743: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Subread> How to use <\/a>\n<!-- Time to render notes section of link id 23743: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23743: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/homonecloco\/subsampler\" id=\"link-24545\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">subsampler<\/a>\n<!-- Time to render name section of link id 24545: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Small tool to subsample fasta and fastq files.<\/p>\n<!-- Time to render link large description section of link id 24545: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24545: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24545: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/sumaclust\" id=\"link-23973\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sumaclust<\/a>\n<!-- Time to render name section of link id 23973: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast and exact clustering of sequences.<\/p>\n<!-- Time to render link large description section of link id 23973: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sumaclust> How to use <\/a>\n<!-- Time to render notes section of link id 23973: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23973: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/sumatra\/wikis\/home\" id=\"link-23744\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sumatra<\/a>\n<!-- Time to render name section of link id 23744: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Sumatra was developed by the LECA and aims to compute a great deal of sequence similarities in a fast and exact way, based on the length of the Longest Common Subsequence (LCS) between two sequences. Sequence clustering based on similarities is also available through Sumaclust.<\/p>\n<!-- Time to render link large description section of link id 23744: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sumatra> How to use <\/a>\n<!-- Time to render notes section of link id 23744: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23744: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/metageni\/SUPER-FOCUS\" id=\"link-24546\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SUPER-FOCUS<\/a>\n<!-- Time to render name section of link id 24546: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool for agile functional analysis of metagenomic data.<\/p>\n<!-- Time to render link large description section of link id 24546: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24546: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24546: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/dportik\/SuperCRUNCH\" id=\"link-24547\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SuperCRUNCH<\/a>\n<!-- Time to render name section of link id 24547: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and\/or local sequence data.<\/p>\n<!-- Time to render link large description section of link id 24547: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24547: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24547: 0.00052785873413086 --> \n<tr><td><a href=\"http:\/\/support.10xgenomics.com\/de-novo-assembly\/software\/overview\/welcome\" id=\"link-23813\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Supernova<\/a>\n<!-- Time to render name section of link id 23813: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source.<\/p>\n<!-- Time to render link large description section of link id 23813: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23813: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23813: 0.00053977966308594 --> \n<tr><td><a href=\"https:\/\/github.com\/vbar\/superstring\" id=\"link-24548\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">superstring<\/a>\n<!-- Time to render name section of link id 24548: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Greedy approximation of the shortest common superstring<\/p>\n<!-- Time to render link large description section of link id 24548: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_superstring> How to use <\/a>\n<!-- Time to render notes section of link id 24548: 1.9073486328125E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24548: 0.00055313110351562 --> \n<tr><td><a href=\"https:\/\/github.com\/deepomicslab\/SuperTAD\" id=\"link-24549\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SuperTAD<\/a>\n<!-- Time to render name section of link id 24549: 8.1062316894531E-6 --> \n<\/td>\n<td><p>SuperTAD is an open-source command-line TAD detection package written in C++. It takes either raw or normalized Hi-C contact maps as inputs.<\/p>\n<!-- Time to render link large description section of link id 24549: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SuperTAD> How to use <\/a>\n<!-- Time to render notes section of link id 24549: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24549: 0.00052404403686523 --> \n<tr><td><a href=\"https:\/\/github.com\/comprna\/SUPPA\" id=\"link-23970\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SUPPA<\/a>\n<!-- Time to render name section of link id 23970: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.<\/p>\n<!-- Time to render link large description section of link id 23970: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SUPPA> How to use <\/a>\n<!-- Time to render notes section of link id 23970: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23970: 0.00051307678222656 --> \n<tr><td><a href=\"https:\/\/github.com\/novoic\/surfboard\" id=\"link-26031\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Surfboard<\/a>\n<!-- Time to render name section of link id 26031: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A Python package for modern audio feature extraction.<\/p>\n<!-- Time to render link large description section of link id 26031: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Surfboard> How to use <\/a>\n<!-- Time to render notes section of link id 26031: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26031: 0.00052404403686523 --> \n<tr><td><a href=\"https:\/\/github.com\/fritzsedlazeck\/SURVIVOR\" id=\"link-24017\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SURVIVOR<\/a>\n<!-- Time to render name section of link id 24017: 6.9141387939453E-6 --> \n<\/td>\n<td><p>SURVIVOR is a tool set for simulating\/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.<\/p>\n<!-- Time to render link large description section of link id 24017: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SURVIVOR> How to use <\/a>\n<!-- Time to render notes section of link id 24017: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24017: 0.00050902366638184 --> \n<tr><td><a href=\"https:\/\/github.com\/walaj\/svaba\" id=\"link-24095\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SvABA<\/a>\n<!-- Time to render name section of link id 24095: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Structural variation and indel detection by local assembly<\/p>\n<!-- Time to render link large description section of link id 24095: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SvABA> How to use <\/a>\n<!-- Time to render notes section of link id 24095: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24095: 0.00044798851013184 --> \n<tr><td><a href=\"https:\/\/github.com\/nhansen\/SVanalyzer\" id=\"link-24550\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVanalyzer<\/a>\n<!-- Time to render name section of link id 24550: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tools for the analysis of structural variation in genomes.<\/p>\n<!-- Time to render link large description section of link id 24550: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24550: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24550: 0.0002140998840332 --> \n<tr><td><a href=\"http:\/\/svdetect.sourceforge.net\/Site\/Home.html\" id=\"link-24014\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVDetect<\/a>\n<!-- Time to render name section of link id 24014: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24014: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24014: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24014: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/eldariont\/svim\" id=\"link-24103\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVIM<\/a>\n<!-- Time to render name section of link id 24103: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SVIM is a structural variant caller for long reads. It is able to detect, classify and genotype five different classes of structural variants.<\/p>\n<!-- Time to render link large description section of link id 24103: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVIM> How to use <\/a>\n<!-- Time to render notes section of link id 24103: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24103: 0.0002138614654541 --> \n<tr><td><a href=\"https:\/\/github.com\/eldariont\/svim-asm\" id=\"link-24857\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVIM-asm<\/a>\n<!-- Time to render name section of link id 24857: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SVIM-asm (pronounced SWIM-assem) is a structural variant caller for haploid or diploid genome-genome alignments.<\/p>\n<!-- Time to render link large description section of link id 24857: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVIM-asm> How to use <\/a>\n<!-- Time to render notes section of link id 24857: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24857: 0.0002129077911377 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/svimmer\" id=\"link-24551\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">svimmer<\/a>\n<!-- Time to render name section of link id 24551: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Merges similar SVs from multiple single sample VCF files. The tool was written for merging SVs discovered using Manta calls, but should support (almost) any SV VCFs.<\/p>\n<!-- Time to render link large description section of link id 24551: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24551: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24551: 0.0002140998840332 --> \n<tr><td><a href=\"https:\/\/github.com\/llecompte\/SVJedi\" id=\"link-24552\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi<\/a>\n<!-- Time to render name section of link id 24552: 2.8610229492188E-6 --> \n<\/td>\n<td><p>SVJedi is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24552: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24552: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24552: 0.00022578239440918 --> \n<tr><td><a href=\"https:\/\/github.com\/SandraLouise\/SVJedi-graph\" id=\"link-24752\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi-graph<\/a>\n<!-- Time to render name section of link id 24752: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SVJedi-graph is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24752: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVJedi-graph> How to use <\/a>\n<!-- Time to render notes section of link id 24752: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24752: 0.00021100044250488 --> \n<tr><td><a href=\"https:\/\/svmerge.sourceforge.net\/\" id=\"link-25315\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVMerge<\/a>\n<!-- Time to render name section of link id 25315: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly.<\/p>\n<!-- Time to render link large description section of link id 25315: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVMerge> How to use <\/a>\n<!-- Time to render notes section of link id 25315: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25315: 0.00022482872009277 --> \n<tr><td><a href=\"https:\/\/github.com\/hall-lab\/svtyper\" id=\"link-23832\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">svtyper<\/a>\n<!-- Time to render name section of link id 23832: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Bayesian genotyper for structural variants.<\/p>\n<!-- Time to render link large description section of link id 23832: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVTyper> How to use <\/a>\n<!-- Time to render notes section of link id 23832: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23832: 0.00021100044250488 --> \n<tr><td><a href=\"https:\/\/github.com\/torognes\/swarm\" id=\"link-23881\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">swarm<\/a>\n<!-- Time to render name section of link id 23881: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A robust and fast clustering method for amplicon-based studies.<\/p>\n<!-- Time to render link large description section of link id 23881: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_swarm> How to use <\/a>\n<!-- Time to render notes section of link id 23881: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23881: 0.00021600723266602 --> \n<tr><td><a href=\"http:\/\/pop-gen.eu\/wordpress\/software\/sweed\" id=\"link-24553\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SweeD<\/a>\n<!-- Time to render name section of link id 24553: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A parallel and checkpointable tool that implements a composite likelihood ratio test for detecting selective sweeps. SweeD is based on the SweepFinder algorithm (Nielsen et al. 2005). SweeD can calculate the theoretical SFS of a given demographic model (stepwise changes or with an exponential growth phase + stepwise changes) by using the method by \u017divkovi\u0107 and Stephan (2011).<\/p>\n<!-- Time to render link large description section of link id 24553: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SweeD> How to use <\/a>\n<!-- Time to render notes section of link id 24553: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24553: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/bluenote-1577\/sylph\" id=\"link-25651\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sylph<\/a>\n<!-- Time to render name section of link id 25651: 3.0994415283203E-6 --> \n<\/td>\n<td><p>sylph is a program that performs ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples.<\/p>\n<!-- Time to render link large description section of link id 25651: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sylph> How to use <\/a>\n<!-- Time to render notes section of link id 25651: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25651: 0.00020885467529297 --> \n<tr><td><a href=\"https:\/\/github.com\/PombertLab\/SYNY\" id=\"link-25700\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SYNY<\/a>\n<!-- Time to render name section of link id 25700: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The SYNY pipeline investigates gene collinearity (synteny) between genomes by reconstructing clusters from conserved pairs of protein-coding genes identified from DIAMOND homology searches. It also infers collinearity from pairwise genome alignments with minimap2 or MashMap3.<\/p>\n<!-- Time to render link large description section of link id 25700: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SYNY> How to use <\/a>\n<!-- Time to render notes section of link id 25700: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25700: 0.00022315979003906 --> \n<tr><td><a href=\"https:\/\/schneebergerlab.github.io\/syri\/\" id=\"link-24554\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SyRI<\/a>\n<!-- Time to render name section of link id 24554: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA).<\/p>\n<!-- Time to render link large description section of link id 24554: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SyRI> How to use <\/a>\n<!-- Time to render notes section of link id 24554: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24554: 0.00017690658569336 --> \n<tr><td><a href=\"http:\/\/www.tcoffee.org\/Projects\/tcoffee\" id=\"link-23745\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T-Coffee<\/a>\n<!-- Time to render name section of link id 23745: 1.9073486328125E-6 --> \n<\/td>\n<td><p>T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignmen.<\/p>\n<!-- Time to render link large description section of link id 23745: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_T-Coffee> How to use <\/a>\n<!-- Time to render notes section of link id 23745: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23745: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/GonzalezLab\/T-lex3\" id=\"link-24555\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T-lex<\/a>\n<!-- Time to render name section of link id 24555: 3.0994415283203E-6 --> \n<\/td>\n<td><p>T-lex is a computational pipeline that detects presence and\/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data.<\/p>\n<!-- Time to render link large description section of link id 24555: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24555: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24555: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/mourisl\/T1K\" id=\"link-26025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T1K<\/a>\n<!-- Time to render name section of link id 26025: 1.9073486328125E-6 --> \n<\/td>\n<td><p>T1K (The ONE genotyper for Kir and HLA) is a computational tool to infer the alleles for the polymorphic genes such as KIR and HLA. T1K calculates the allele abundances based on the RNA-seq\/WES\/WGS read alignments on the provided allele reference sequences. The abundances are used to pick the true alleles for each gene. T1K provides the post analysis steps, including novel SNP detection and single-cell representation. T1K supports both single-end and paired-end sequencing data with any read length.<\/p>\n<!-- Time to render link large description section of link id 26025: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_T1K> How to use <\/a>\n<!-- Time to render notes section of link id 26025: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26025: 0.00020098686218262 --> \n<tr><td><a href=\"http:\/\/sourceforge.net\/projects\/samtools\/files\/tabix\/\" id=\"link-23746\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">tabix<\/a>\n<!-- Time to render name section of link id 23746: 2.8610229492188E-6 --> \n<\/td>\n<td><p>TAB-delimited file IndeXer. Useful for vcfTools.<\/p>\n<!-- Time to render link large description section of link id 23746: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in bcftools and samtools\n<!-- Time to render notes section of link id 23746: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23746: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/tacorna\/taco\" id=\"link-25534\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TACO<\/a>\n<!-- Time to render name section of link id 25534: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Multi-sample transcriptome assembly from RNA-Seq.<\/p>\n<!-- Time to render link large description section of link id 25534: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TACO> How to use <\/a>\n<!-- Time to render notes section of link id 25534: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25534: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/jonchang\/tact\" id=\"link-24556\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TACT<\/a>\n<!-- Time to render name section of link id 24556: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models<\/p>\n<!-- Time to render link large description section of link id 24556: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24556: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24556: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/tandem.bu.edu\/trf\/trf.html\" id=\"link-23747\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tandem Repeats Finder<\/a>\n<!-- Time to render name section of link id 23747: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides.<\/p>\n<!-- Time to render link large description section of link id 23747: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TRF> How to use <\/a>\n<!-- Time to render notes section of link id 23747: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23747: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/arefeen\/TAPAS\" id=\"link-25322\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TAPAS<\/a>\n<!-- Time to render name section of link id 25322: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Tool for Alternative Polyadenylation Site Analysis.<\/p>\n<!-- Time to render link large description section of link id 25322: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TAPAS> How to use <\/a>\n<!-- Time to render notes section of link id 25322: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25322: 0.00016283988952637 --> \n<tr><td><a href=\"https:\/\/github.com\/johnomics\/tapestry\" id=\"link-24094\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tapestry<\/a>\n<!-- Time to render name section of link id 24094: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tapestry is a tool to validate and edit small eukaryotic genome assemblies using long sequence reads. It is designed to help identify complete chromosomes, symbionts, haplotypes, complex features and errors in close-to-complete genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24094: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24094: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24094: 0.00020408630371094 --> \n<tr><td><a href=\"https:\/\/github.com\/BilkentCompGen\/tardis\" id=\"link-24851\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TARDIS<\/a>\n<!-- Time to render name section of link id 24851: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Toolkit for automated and rapid discovery of structural variants.<\/p>\n<!-- Time to render link large description section of link id 24851: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24851: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24851: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/services.healthtech.dtu.dk\/service.php?TargetP-2.0\" id=\"link-24558\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TargetP<\/a>\n<!-- Time to render name section of link id 24558: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TargetP-2.0 server predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (lTP). For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.<\/p>\n<!-- Time to render link large description section of link id 24558: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TargetP> How to use <\/a>\n<!-- Time to render notes section of link id 24558: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24558: 0.00016403198242188 --> \n<tr><td><a href=\"http:\/\/www.maizegenetics.net\/tassel\" id=\"link-23748\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TASSEL<\/a>\n<!-- Time to render name section of link id 23748: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Trait Analysis by aSSociation, Evolution and Linkage. TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization for large sets of data.<\/p>\n<!-- Time to render link large description section of link id 23748: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TASSEL> How to use <\/a>\n<!-- Time to render notes section of link id 23748: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23748: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/bioinf.shenwei.me\/taxonkit\/\" id=\"link-24648\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TaxonKit<\/a>\n<!-- Time to render name section of link id 24648: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A Practical and Efficient NCBI Taxonomy Toolkit<\/p>\n<!-- Time to render link large description section of link id 24648: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TaxonKit> How to use <\/a>\n<!-- Time to render notes section of link id 24648: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24648: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/github.com\/CJ-Chen\/TBtools-II\" id=\"link-25247\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TBtools-II<\/a>\n<!-- Time to render name section of link id 25247: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GUI\/CommandLine Tool Box for biologistists to utilize NGS data.<\/p>\n<!-- Time to render link large description section of link id 25247: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TBtools-II> How to use <\/a>\n<!-- Time to render notes section of link id 25247: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25247: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/urgi-anagen\/te_finder\" id=\"link-25695\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TE_finder<\/a>\n<!-- Time to render name section of link id 25695: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.<\/p>\n<!-- Time to render link large description section of link id 25695: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TE_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25695: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25695: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/cancerit\/telomerecat\" id=\"link-26023\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Telomerecat<\/a>\n<!-- Time to render name section of link id 26023: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Telomerecat is a tool for estimating the average telomere length (TL) for a paired end, whole genome sequencing (WGS) sample.<\/p>\n<!-- Time to render link large description section of link id 26023: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.9.18\n<!-- Time to render notes section of link id 26023: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26023: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/pypi.org\/project\/telomerehunter\/\" id=\"link-26022\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TelomereHunter<\/a>\n<!-- Time to render name section of link id 26022: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TelomereHunter extracts, sorts and analyses telomeric reads from WGS Data.<\/p>\n<!-- Time to render link large description section of link id 26022: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-2.7.18\n<!-- Time to render notes section of link id 26022: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26022: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/zhangrengang\/TEsorter\" id=\"link-24560\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TEsorter<\/a>\n<!-- Time to render name section of link id 24560: 0.00033092498779297 --> \n<\/td>\n<td><p>It is coded for LTR_retriever to classify long terminal repeat retrotransposons (LTR-RTs) at first. It can also be used to classify any other TE sequences, including Class I and Class II elements which are covered by the REXdb database.<\/p>\n<!-- Time to render link large description section of link id 24560: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TEsorter> How to use <\/a>\n<!-- Time to render notes section of link id 24560: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24560: 0.00051999092102051 --> \n<tr><td><a href=\"https:\/\/github.com\/Dfam-consortium\/TETools\" id=\"link-25666\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TETools<\/a>\n<!-- Time to render name section of link id 25666: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg. This container is an easy way to get a minimal yet fully functional installation of RepeatMasker and RepeatModeler and is additionally useful for testing or reproducibility purposes.<\/p>\n<!-- Time to render link large description section of link id 25666: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TETools> How to use <\/a>\n<!-- Time to render notes section of link id 25666: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25666: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/www.tug.org\/texlive\" id=\"link-24561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TexLive<\/a>\n<!-- Time to render name section of link id 24561: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TeX Live is intended to be a straightforward way to get up and running with the TeX document production system.<\/p>\n<!-- Time to render link large description section of link id 24561: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24561: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24561: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/tgicl\/\" id=\"link-23609\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TGICL<\/a>\n<!-- Time to render name section of link id 23609: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This package automates clustering and assembly of a large EST\/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's<i> megablast <\/i>, and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3.<\/p>\n<!-- Time to render link large description section of link id 23609: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TGICL> How to use <\/a>\n<!-- Time to render notes section of link id 23609: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23609: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/TGSGapFiller\" id=\"link-24562\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TGSGapFiller<\/a>\n<!-- Time to render name section of link id 24562: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A gap filling tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.<\/p>\n<!-- Time to render link large description section of link id 24562: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24562: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24562: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/Tiberius\" id=\"link-25518\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tiberius<\/a>\n<!-- Time to render name section of link id 25518: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tiberius is a deep learning-based ab initio gene structure prediction tool that end-to-end integrates convolutional and long short-term memory layers with a differentiable HMM layer.<\/p>\n<!-- Time to render link large description section of link id 25518: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Tiberius> How to use <\/a>\n<!-- Time to render notes section of link id 25518: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25518: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/tolkit\/telomeric-identifier\" id=\"link-24563\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">tidk<\/a>\n<!-- Time to render name section of link id 24563: 3.0994415283203E-6 --> \n<\/td>\n<td><p>tidk is a toolkit to identify and visualise telomeric repeats for the Darwin Tree of Life genomes.<\/p>\n<!-- Time to render link large description section of link id 24563: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_tidk> How to use <\/a>\n<!-- Time to render notes section of link id 24563: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24563: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/bcgsc.github.io\/tigmint\/\" id=\"link-23962\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tigmint<\/a>\n<!-- Time to render name section of link id 23962: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tigmint identifies and corrects misassemblies using linked reads from 10x Genomics Chromium.<\/p>\n<!-- Time to render link large description section of link id 23962: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23962: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23962: 0.00022196769714355 --> \n<tr><td><a href=\"https:\/\/github.com\/danimfernandes\/tkgwv2\" id=\"link-24564\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TKGWV2<\/a>\n<!-- Time to render name section of link id 24564: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TKGWV2 is a pipeline to estimate biological relatedness (1st, 2nd, and unrelated degrees) between individuals specifically aimed at ultra-low coverage ancient DNA data obtained from whole genome sequencing.<\/p>\n<!-- Time to render link large description section of link id 24564: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TKGWV2> How to use <\/a>\n<!-- Time to render notes section of link id 24564: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24564: 0.00016498565673828 --> \n<tr><td><a href=\"http:\/\/www.cbs.dtu.dk\/cgi-bin\/nph-sw_request?tmhmm\" id=\"link-23767\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TMHMM<\/a>\n<!-- Time to render name section of link id 23767: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Prediction of transmembrane helices in proteins.<\/p>\n<!-- Time to render link large description section of link id 23767: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TMHMM> How to use <\/a>\n<!-- Time to render notes section of link id 23767: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23767: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/danillo-alvarenga\/tn3-ta_finder\" id=\"link-25339\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tn3+TA_finder<\/a>\n<!-- Time to render name section of link id 25339: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tn3 Transposon\/Toxin Finder (Tn3+TA_finder) is a program for the automatic prediction of transposable elements of the Tn3 family associated with type II toxin and antitoxin pairs in bacteria and archaea.<\/p>\n<!-- Time to render link large description section of link id 25339: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Tn3-TA_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25339: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25339: 0.00078201293945312 --> \n<tr><td><a href=\"https:\/\/github.com\/danillo-alvarenga\/tncomp_finder\" id=\"link-25338\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TnComp_finder<\/a>\n<!-- Time to render name section of link id 25338: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Composite Transposon Finder (TnComp_finder) is a program for the prediction of putative composite transposons in bacterial and archaeal genomes based on insertion sequence replicas in a relatively short span.<\/p>\n<!-- Time to render link large description section of link id 25338: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TnComp_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25338: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25338: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/loosolab\/TOBIAS\" id=\"link-24565\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TOBIAS<\/a>\n<!-- Time to render name section of link id 24565: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.<\/p>\n<!-- Time to render link large description section of link id 24565: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TOBIAS> How to use <\/a>\n<!-- Time to render notes section of link id 24565: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24565: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/hillerlab\/TOGA\" id=\"link-25357\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TOGA<\/a>\n<!-- Time to render name section of link id 25357: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost.<\/p>\n<!-- Time to render link large description section of link id 25357: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TOGA> How to use <\/a>\n<!-- Time to render notes section of link id 25357: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25357: 0.00019097328186035 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/tombo\" id=\"link-24011\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tombo<\/a>\n<!-- Time to render name section of link id 24011: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24011: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24011: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24011: 0.00017595291137695 --> \n<tr><td><a href=\"http:\/\/www.topali.org\" id=\"link-24566\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TOPALI-v2<\/a>\n<!-- Time to render name section of link id 24566: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops.<\/p>\n<!-- Time to render link large description section of link id 24566: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24566: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24566: 0.00017380714416504 --> \n<tr><td><a href=\"http:\/\/tophat.cbcb.umd.edu\" id=\"link-23749\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tophat<\/a>\n<!-- Time to render name section of link id 23749: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner <a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\/\" rel=\"nofollow\">Bowtie<\/a>, and then analyzes the mapping results to identify splice junctions between exons.<\/p>\n<!-- Time to render link large description section of link id 23749: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Tophat> How to use <\/a>\n<!-- Time to render notes section of link id 23749: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23749: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/toulbar2\/toulbar2\" id=\"link-24567\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">toulbar2<\/a>\n<!-- Time to render name section of link id 24567: 2.8610229492188E-6 --> \n<\/td>\n<td><p>toulbar2 is an open-source black-box C++ optimizer for cost function networks and discrete additive graphical models. It can read a variety of formats.<\/p>\n<!-- Time to render link large description section of link id 24567: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_toulbar2> How to use <\/a>\n<!-- Time to render notes section of link id 24567: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24567: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/TPMCalculator\" id=\"link-24071\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TPMCalculator<\/a>\n<!-- Time to render name section of link id 24071: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.<\/p>\n<!-- Time to render link large description section of link id 24071: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TPMCalculator> How to use <\/a>\n<!-- Time to render notes section of link id 24071: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24071: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/www.gear-genomics.com\/docs\/tracy\/\" id=\"link-24568\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tracy<\/a>\n<!-- Time to render name section of link id 24568: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tracy is an efficient and versatile command-line application to basecall, align, assemble and deconvolute Sanger Chromatogram trace files.<\/p>\n<!-- Time to render link large description section of link id 24568: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24568: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24568: 0.00017619132995605 --> \n<tr><td><a href=\"http:\/\/transdecoder.github.io\/\" id=\"link-23750\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TransDecoder<\/a>\n<!-- Time to render name section of link id 23750: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.<\/p>\n<!-- Time to render link large description section of link id 23750: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TransDecoder> How to use <\/a>\n<!-- Time to render notes section of link id 23750: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23750: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/sestaton.github.io\/Transposome\/\" id=\"link-24569\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Transposome<\/a>\n<!-- Time to render name section of link id 24569: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Transposome is a command line application to annotate transposable elements from paired-end whole genome shotgun data.<\/p>\n<!-- Time to render link large description section of link id 24569: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24569: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24569: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/DerKevinRiehl\/transposon_annotation_tools\" id=\"link-24570\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">transposon_annotation_tools<\/a>\n<!-- Time to render name section of link id 24570: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of bioconda packages for transposon annotation and transposon feature annotation in nucleotide sequences. transposon_annotation_tools is part of TransposonUltimate. The package includes a series of transposable element discovery tools, such as: MUSTv2, HelitronScanner, SineFinder, MiteTracker, MiteFinderII, SineScan, TirVish, LtrHarvest, RepeatModeler, TransposonPSI, and TransposonProteinNCBICDD1000. You can then use these tools independently.<\/p>\n<!-- Time to render link large description section of link id 24570: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_transposon_annotation_tools> How to use <\/a>\n<!-- Time to render notes section of link id 24570: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24570: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/DerKevinRiehl\/transposon_classifier_rfsb\" id=\"link-25186\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">transposon_classifier_rfsb<\/a>\n<!-- Time to render name section of link id 25186: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Transposon classification tool for nucleotide sequence classification, providing classification, model training and prediction evaluation. <em>RFSB<\/em> is part of <a href=\"https:\/\/github.com\/DerKevinRiehl\/TransposonUltimate\">TransposonUltimate<\/a>.<\/p>\n<!-- Time to render link large description section of link id 25186: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_transposon_classifier_rfsb> How to use <\/a>\n<!-- Time to render notes section of link id 25186: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25186: 0.00016307830810547 --> \n<tr><td><a href=\"http:\/\/hibberdlab.com\/transrate\/index.html\" id=\"link-23775\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Transrate<\/a>\n<!-- Time to render name section of link id 23775: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Transrate is software for de-novo transcriptome assembly quality analysis.<\/p>\n<!-- Time to render link large description section of link id 23775: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Transrate> How to use <\/a>\n<!-- Time to render notes section of link id 23775: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23775: 0.00020599365234375 --> \n<tr><td><a href=\"https:\/\/github.com\/vlothec\/TRASH\" id=\"link-25165\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TRASH<\/a>\n<!-- Time to render name section of link id 25165: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Tandem Repeat Annotation and Structural Hierarchy: a package to identify and extract tandem repeats in genome sequences and investigate their higher order structures.<\/p>\n<!-- Time to render link large description section of link id 25165: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TRASH> How to use <\/a>\n<!-- Time to render notes section of link id 25165: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25165: 0.00018978118896484 --> \n<tr><td><a href=\"http:\/\/treesoft.sourceforge.net\/treebest.shtml\" id=\"link-23843\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeBeST<\/a>\n<!-- Time to render name section of link id 23843: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.<\/p>\n<!-- Time to render link large description section of link id 23843: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23843: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23843: 0.00016593933105469 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/treemix\/\" id=\"link-23751\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeMix<\/a>\n<!-- Time to render name section of link id 23751: 2.8610229492188E-6 --> \n<\/td>\n<td><p><i>TreeMix<\/i> is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.<\/p>\n<!-- Time to render link large description section of link id 23751: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TreeMix> How to use <\/a>\n<!-- Time to render notes section of link id 23751: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23751: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/blackrim\/treePL\" id=\"link-23885\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">treePL<\/a>\n<!-- Time to render name section of link id 23885: 2.1457672119141E-6 --> \n<\/td>\n<td><p>treePL is a phylogenetic penalized likelihood program.<\/p>\n<!-- Time to render link large description section of link id 23885: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23885: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23885: 0.00019216537475586 --> \n<tr><td><a href=\"https:\/\/github.com\/uym2\/TreeShrink\" id=\"link-24084\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeShrink<\/a>\n<!-- Time to render name section of link id 24084: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees.<\/p>\n<!-- Time to render link large description section of link id 24084: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TreeShrink> How to use <\/a>\n<!-- Time to render notes section of link id 24084: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24084: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/neherlab\/treetime\" id=\"link-24748\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeTime<\/a>\n<!-- Time to render name section of link id 24748: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction.<\/p>\n<!-- Time to render link large description section of link id 24748: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24748: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24748: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/\" id=\"link-23752\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trim Galore<\/a>\n<!-- Time to render name section of link id 23752: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.<\/p>\n<!-- Time to render link large description section of link id 23752: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TrimGalore> How to use <\/a>\n<!-- Time to render notes section of link id 23752: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23752: 0.00017690658569336 --> \n<tr><td><a href=\"http:\/\/trimal.cgenomics.org\/introduction\" id=\"link-23753\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">trimAl<\/a>\n<!-- Time to render name section of link id 23753: 3.0994415283203E-6 --> \n<\/td>\n<td><p>trimAl: a tool for automated alignment trimmin<\/p>\n<!-- Time to render link large description section of link id 23753: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_trimAl> How to use <\/a>\n<!-- Time to render notes section of link id 23753: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23753: 0.00017714500427246 --> \n<tr><td><a href=\"http:\/\/www.usadellab.org\/cms\/?page=trimmomatic%20\" id=\"link-23754\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trimmomatic<\/a>\n<!-- Time to render name section of link id 23754: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.<\/p>\n<!-- Time to render link large description section of link id 23754: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Trimmomatic> How to use <\/a>\n<!-- Time to render notes section of link id 23754: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23754: 0.00017619132995605 --> \n<tr><td><a href=\"http:\/\/trinityrnaseq.sourceforge.net\/\" id=\"link-23755\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">trinityrnaseq<\/a>\n<!-- Time to render name section of link id 23755: 1.9073486328125E-6 --> \n<\/td>\n<td><div class=\"para\">Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.<\/div>\n<!-- Time to render link large description section of link id 23755: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_trinityrnaseq> How to use <\/a>\n<!-- Time to render notes section of link id 23755: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23755: 0.00018596649169922 --> \n<tr><td><a href=\"http:\/\/trinotate.sourceforge.net\/\" id=\"link-23756\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trinotate<\/a>\n<!-- Time to render name section of link id 23756: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.<\/p>\n<!-- Time to render link large description section of link id 23756: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23756: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23756: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/tRNAscan-SE\/\" id=\"link-23757\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">tRNAscan-SE<\/a>\n<!-- Time to render name section of link id 23757: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Search for tRNA genes in genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 23757: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_tRNAscan-SE> How to use <\/a>\n<!-- Time to render notes section of link id 23757: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23757: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/spiralgenetics\/truvari\" id=\"link-24056\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Truvari<\/a>\n<!-- Time to render name section of link id 24056: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Structural variant comparison tool for VCFs<\/p>\n<!-- Time to render link large description section of link id 24056: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Truvari> How to use <\/a>\n<!-- Time to render notes section of link id 24056: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24056: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Trycycler\" id=\"link-24571\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trycycler<\/a>\n<!-- Time to render name section of link id 24571: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 24571: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Trycycler> How to use <\/a>\n<!-- Time to render notes section of link id 24571: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24571: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/TSEBRA\" id=\"link-24572\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TSEBRA<\/a>\n<!-- Time to render name section of link id 24572: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start\/stop codons. It was developed to combine BRAKER11 and BRAKER22 predicitons to increase their accuracies.<\/p>\n<!-- Time to render link large description section of link id 24572: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TSEBRA> How to use <\/a>\n<!-- Time to render notes section of link id 24572: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24572: 0.00019216537475586 --> \n<tr><td><a href=\"https:\/\/github.com\/simonhmartin\/twisst\" id=\"link-25333\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Twisst<\/a>\n<!-- Time to render name section of link id 25333: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Topology weighting by iterative sampling of sub-trees.<\/p>\n<!-- Time to render link large description section of link id 25333: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Twisst> How to use <\/a>\n<!-- Time to render notes section of link id 25333: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25333: 0.00019311904907227 --> \n<tr><td><a href=\"https:\/\/github.com\/ksahlin\/ultra\" id=\"link-24322\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">uLTRA<\/a>\n<!-- Time to render name section of link id 24322: 2.8610229492188E-6 --> \n<\/td>\n<td><p>uLTRA is a tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations.<\/p>\n<!-- Time to render link large description section of link id 24322: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_uLTRA> How to use <\/a>\n<!-- Time to render notes section of link id 24322: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24322: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/hoffmanlab\/umap\/src\/default\/\" id=\"link-24573\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Umap<\/a>\n<!-- Time to render name section of link id 24573: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The free umap software package efficiently identifies uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite converted genome (methylome).<\/p>\n<!-- Time to render link large description section of link id 24573: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24573: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24573: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/CGATOxford\/UMI-tools\" id=\"link-24092\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">UMI-tools<\/a>\n<!-- Time to render name section of link id 24092: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tools for handling Unique Molecular Identifiers in NGS data sets<\/p>\n<!-- Time to render link large description section of link id 24092: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_UMI-tools> How to use <\/a>\n<!-- Time to render notes section of link id 24092: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24092: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Unicycler\" id=\"link-23948\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Unicycler<\/a>\n<!-- Time to render name section of link id 23948: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Unicycler is an assembly pipeline for bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 23948: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Unicycler> How to use <\/a>\n<!-- Time to render notes section of link id 23948: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23948: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/unimap\" id=\"link-24822\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Unimap<\/a>\n<!-- Time to render name section of link id 24822: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment.<\/p>\n<!-- Time to render link large description section of link id 24822: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Unimap> How to use <\/a>\n<!-- Time to render notes section of link id 24822: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24822: 0.00016522407531738 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/unique-kmer-counts\" id=\"link-25441\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">unique-kmer-counts<\/a>\n<!-- Time to render name section of link id 25441: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This program calculates the number of distinct k-mers for each sequence record in a fasta file and divides it by the total number of k-mers in that record.<\/p>\n<!-- Time to render link large description section of link id 25441: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_unique-kmer-counts> How to use <\/a>\n<!-- Time to render notes section of link id 25441: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25441: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/bacpop\/unitig-caller\" id=\"link-25656\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">unitig-caller<\/a>\n<!-- Time to render name section of link id 25656: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Methods to determine sequence element (unitig) presence\/absence.<\/p>\n<!-- Time to render link large description section of link id 25656: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_unitig-caller> How to use <\/a>\n<!-- Time to render notes section of link id 25656: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25656: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/www.rarlab.com\/rar_add.htm\" id=\"link-26120\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">UnRAR<\/a>\n<!-- Time to render name section of link id 26120: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Easily extract RAR files.<\/p>\n<!-- Time to render link large description section of link id 26120: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_UnRAR> How to use <\/a>\n<!-- Time to render notes section of link id 26120: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26120: 0.00016283988952637 --> \n<tr><td><a href=\"http:\/\/www.drive5.com\/usearch\/\" id=\"link-23758\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">USEARCH<\/a>\n<!-- Time to render name section of link id 23758: 1.9073486328125E-6 --> \n<\/td>\n<td><p>USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.<\/p>\n<!-- Time to render link large description section of link id 23758: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_USEARCH> How to use <\/a>\n<!-- Time to render notes section of link id 23758: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23758: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/Aveglia\/vAMPirus\" id=\"link-25599\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vAMPirus<\/a>\n<!-- Time to render name section of link id 25599: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.<\/p>\n<!-- Time to render link large description section of link id 25599: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vAMPirus> How to use <\/a>\n<!-- Time to render notes section of link id 25599: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25599: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/github.com\/AstraZeneca-NGS\/VarDict\" id=\"link-24574\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VarDict<\/a>\n<!-- Time to render name section of link id 24574: 1.9073486328125E-6 --> \n<\/td>\n<td><p>VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files.<\/p>\n<!-- Time to render link large description section of link id 24574: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24574: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24574: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/treangenlab\/variabel\" id=\"link-24575\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Variabel<\/a>\n<!-- Time to render name section of link id 24575: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A novel approach and method for intrahost variant detection, which outperforms existing ONT variant callers.<\/p>\n<!-- Time to render link large description section of link id 24575: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24575: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24575: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/JiaoLab2021\/varigraph\" id=\"link-26195\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">varigraph<\/a>\n<!-- Time to render name section of link id 26195: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes.<\/p>\n<!-- Time to render link large description section of link id 26195: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_varigraph> How to use <\/a>\n<!-- Time to render notes section of link id 26195: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26195: 0.00015902519226074 --> \n<tr><td><a href=\"http:\/\/varscan.sourceforge.net\/\" id=\"link-23759\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VarScan<\/a>\n<!-- Time to render name section of link id 23759: 1.9073486328125E-6 --> \n<\/td>\n<td><p>VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.<\/p>\n<!-- Time to render link large description section of link id 23759: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VarScan> How to use <\/a>\n<!-- Time to render notes section of link id 23759: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23759: 0.00016117095947266 --> \n<tr><td><a href=\"https:\/\/github.com\/10XGenomics\/vartrix\" id=\"link-24860\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VarTrix<\/a>\n<!-- Time to render name section of link id 24860: 1.9073486328125E-6 --> \n<\/td>\n<td><p>VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.<\/p>\n<!-- Time to render link large description section of link id 24860: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24860: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24860: 0.0001978874206543 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/CBGR\/jaspar_enrichment\/src\/master\/\" id=\"link-24331\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VAST-TOOLS<\/a>\n<!-- Time to render name section of link id 24331: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Vertebrate Alternative Splicing and Transcription Tools (VAST-TOOLS) is a toolset for profiling and comparing alternative splicing events in RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 24331: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24331: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24331: 0.00021004676818848 --> \n<tr><td><a href=\"https:\/\/github.com\/cc2qe\/vawk\" id=\"link-23839\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vawk<\/a>\n<!-- Time to render name section of link id 23839: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An awk-like VCF parser<\/p>\n<!-- Time to render link large description section of link id 23839: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23839: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23839: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/AndersenLab\/VCF-kit\" id=\"link-24755\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VCF-kit<\/a>\n<!-- Time to render name section of link id 24755: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assorted utilities for the variant call format.<\/p>\n<!-- Time to render link large description section of link id 24755: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24755: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24755: 0.00020003318786621 --> \n<tr><td><a href=\"https:\/\/github.com\/mskcc\/vcf2maf\" id=\"link-24577\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcf2maf<\/a>\n<!-- Time to render name section of link id 24577: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms.<\/p>\n<!-- Time to render link large description section of link id 24577: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcf2maf> How to use <\/a>\n<!-- Time to render notes section of link id 24577: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24577: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/vcflib\/vcflib\" id=\"link-24578\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcflib<\/a>\n<!-- Time to render name section of link id 24578: 3.0994415283203E-6 --> \n<\/td>\n<td><p>C++ library and cmdline tools for parsing and manipulating VCF files.<\/p>\n<!-- Time to render link large description section of link id 24578: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcflib> How to use <\/a>\n<!-- Time to render notes section of link id 24578: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24578: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/biopet\/vcfstats\" id=\"link-26194\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vcfstats<\/a>\n<!-- Time to render name section of link id 26194: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Vcfstats is a tool that can generate metrics from a vcf file.<\/p>\n<!-- Time to render link large description section of link id 26194: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vcfstats> How to use <\/a>\n<!-- Time to render notes section of link id 26194: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26194: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/vcftools.github.io\/index.html\" id=\"link-23760\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VCFtools<\/a>\n<!-- Time to render name section of link id 23760: 3.0994415283203E-6 --> \n<\/td>\n<td><p>VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.<\/p>\n<!-- Time to render link large description section of link id 23760: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VCFtools> How to use <\/a>\n<!-- Time to render notes section of link id 23760: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23760: 0.00019407272338867 --> \n<tr><td><a href=\"http:\/\/velocyto.org\/\" id=\"link-24579\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Velocyto<\/a>\n<!-- Time to render name section of link id 24579: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Package for the analysis of expression dynamics in single cell RNA seq data.<\/p>\n<!-- Time to render link large description section of link id 24579: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_velocyto> How to use <\/a>\n<!-- Time to render notes section of link id 24579: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24579: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/dzerbino\/velvet\" id=\"link-23761\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Velvet<\/a>\n<!-- Time to render name section of link id 23761: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. <br \/>\r\n<br \/>\r\nVelvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.<\/p>\n<!-- Time to render link large description section of link id 23761: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Velvet> How to use <\/a>\n<!-- Time to render notes section of link id 23761: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23761: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/github.com\/vgteam\/vg\" id=\"link-24581\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vg<\/a>\n<!-- Time to render name section of link id 24581: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.<\/p>\n<!-- Time to render link large description section of link id 24581: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vg> How to use <\/a>\n<!-- Time to render notes section of link id 24581: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24581: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/www.tbi.univie.ac.at\/RNA\/#\" id=\"link-23762\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViennaRNA<\/a>\n<!-- Time to render name section of link id 23762: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Vienna RNA package allows RNA Secondary Structure Prediction and Comparison<\/p>\n<!-- Time to render link large description section of link id 23762: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ViennaRNA> How to use <\/a>\n<!-- Time to render notes section of link id 23762: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23762: 0.00018811225891113 --> \n<tr><td><a href=\"https:\/\/github.com\/xie186\/ViewBS\" id=\"link-24582\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViewBS<\/a>\n<!-- Time to render name section of link id 24582: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A powerful toolkit for visualization of high-throughput bisulfite sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24582: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ViewBS> How to use <\/a>\n<!-- Time to render notes section of link id 24582: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24582: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/DeltaGroupNJUPT\/Vina-GPU-2.0\" id=\"link-26149\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vina-GPU-2.0<\/a>\n<!-- Time to render name section of link id 26149: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Vina-GPU 2.0 accelerates AutoDock Vina and its related commonly derived docking methods, such as QuickVina 2 and QuickVina-W with GPUs.<\/p>\n<!-- Time to render link large description section of link id 26149: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vina-GPU-2.0> How to use <\/a>\n<!-- Time to render notes section of link id 26149: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26149: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/XiaohuaZhangLLNL\/VinaLC\" id=\"link-25096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VinaLC<\/a>\n<!-- Time to render name section of link id 25096: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A parallel molecular docking program based on AutoDock Vina.<\/p>\n<!-- Time to render link large description section of link id 25096: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VinaLC> How to use <\/a>\n<!-- Time to render notes section of link id 25096: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25096: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/Matthijnssenslab\/ViPER\" id=\"link-25686\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViPER<\/a>\n<!-- Time to render name section of link id 25686: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Bioinformatics pipeline used in the Laboratory of Viral Metagenomics (KU Leuven) to trim and assemble paired-end Illumina reads, and classify resulting contigs.<\/p>\n<!-- Time to render link large description section of link id 25686: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ViPER> How to use <\/a>\n<!-- Time to render notes section of link id 25686: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25686: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/viquas\/\" id=\"link-24583\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViQuaS<\/a>\n<!-- Time to render name section of link id 24583: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing.<\/p>\n<!-- Time to render link large description section of link id 24583: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24583: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24583: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/single-cell-genetics\/vireo\" id=\"link-25927\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vireoSNP<\/a>\n<!-- Time to render name section of link id 25927: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Vireo: Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.<\/p>\n<!-- Time to render link large description section of link id 25927: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vireoSNP> How to use <\/a>\n<!-- Time to render notes section of link id 25927: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25927: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/github.com\/EBI-Metagenomics\/emg-viral-pipeline\" id=\"link-25366\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VIRify<\/a>\n<!-- Time to render name section of link id 25366: 2.1457672119141E-6 --> \n<\/td>\n<td><p>VIRify is a pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies.<\/p>\n<!-- Time to render link large description section of link id 25366: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VIRify> How to use <\/a>\n<!-- Time to render notes section of link id 25366: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25366: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/jiarong\/VirSorter2\" id=\"link-24584\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VirSorter2<\/a>\n<!-- Time to render name section of link id 24584: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Customizable pipeline to identify viral sequences from (meta)genomic data.<\/p>\n<!-- Time to render link large description section of link id 24584: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ntJoin> How to use <\/a>\n<!-- Time to render notes section of link id 24584: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24584: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/virulencefinder\" id=\"link-24585\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VirulenceFinder<\/a>\n<!-- Time to render name section of link id 24585: 3.0994415283203E-6 --> \n<\/td>\n<td><p>VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available.<\/p>\n<!-- Time to render link large description section of link id 24585: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24585: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24585: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/DrKaiyangZheng\/VITAP\" id=\"link-25764\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VITAP<\/a>\n<!-- Time to render name section of link id 25764: 1.9073486328125E-6 --> \n<\/td>\n<td>The viral taxonomic assignment pipeline \n<!-- Time to render link large description section of link id 25764: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=Howse <\/a>\n<!-- Time to render notes section of link id 25764: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25764: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/atanunq\/viu\" id=\"link-25337\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">viu<\/a>\n<!-- Time to render name section of link id 25337: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A small command-line application to view images from the terminal written in Rust.<\/p>\n<!-- Time to render link large description section of link id 25337: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_viu> How to use <\/a>\n<!-- Time to render notes section of link id 25337: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25337: 0.00017905235290527 --> \n<tr><td><a href=\"http:\/\/www.vmatch.de\" id=\"link-24586\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vmatch<\/a>\n<!-- Time to render name section of link id 24586: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A versatile software tool for e\ufb03ciently solving large scale sequence matching tasks.<\/p>\n<!-- Time to render link large description section of link id 24586: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24586: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24586: 0.00018215179443359 --> \n<tr><td><a href=\"https:\/\/alphacephei.com\/vosk\/\" id=\"link-25808\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vosk<\/a>\n<!-- Time to render name section of link id 25808: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Vosk is an offline open source speech recognition toolkit. It enables speech recognition for 20+ languages and dialects.<\/p>\n<!-- Time to render link large description section of link id 25808: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vosk> How to use <\/a>\n<!-- Time to render notes section of link id 25808: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25808: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/sverre-phd-work\/voyager\/src\/master\/\" id=\"link-25922\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Voyager<\/a>\n<!-- Time to render name section of link id 25922: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Rapid and efficient mapping algorithm for long sequencing reads with insertion- and deletion errors. Mapping long reads in Sorted Motif Distance Space.<\/p>\n<!-- Time to render link large description section of link id 25922: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Voyager> How to use <\/a>\n<!-- Time to render notes section of link id 25922: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25922: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/github.com\/torognes\/vsearch\" id=\"link-23787\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VSEARCH<\/a>\n<!-- Time to render name section of link id 23787: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Versatile open-source tool for metagenomics<\/p>\n<!-- Time to render link large description section of link id 23787: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VSEARCH> How to use <\/a>\n<!-- Time to render notes section of link id 23787: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23787: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/atks\/vt\" id=\"link-25487\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vt<\/a>\n<!-- Time to render name section of link id 25487: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool set for short variant discovery in genetic sequence data.<\/p>\n<!-- Time to render link large description section of link id 25487: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vt> How to use <\/a>\n<!-- Time to render notes section of link id 25487: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25487: 0.00016403198242188 --> \n<tr><td><a href=\"https:\/\/github.com\/bmvdgeijn\/WASP\" id=\"link-25991\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WASP<\/a>\n<!-- Time to render name section of link id 25991: 3.0994415283203E-6 --> \n<\/td>\n<td><p>WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs.<\/p>\n<!-- Time to render link large description section of link id 25991: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WASP> How to use <\/a>\n<!-- Time to render notes section of link id 25991: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25991: 0.00017881393432617 --> \n<tr><td><a href=\"https:\/\/github.com\/adigenova\/wengan\" id=\"link-24587\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Wengan<\/a>\n<!-- Time to render name section of link id 24587: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An accurate and ultra-fast genome assembler<\/p>\n<!-- Time to render link large description section of link id 24587: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24587: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24587: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/smarco\/WFA\" id=\"link-24588\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WFA<\/a>\n<!-- Time to render name section of link id 24588: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.<\/p>\n<!-- Time to render link large description section of link id 24588: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24588: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24588: 0.00037717819213867 --> \n<tr><td><a href=\"https:\/\/github.com\/waveygang\/wfmash\" id=\"link-24589\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wfmash<\/a>\n<!-- Time to render name section of link id 24589: 7.8678131103516E-6 --> \n<\/td>\n<td><p>wfmash is an aligner for pangenomes based on sparse homology mapping and wavefront inception.<\/p>\n<!-- Time to render link large description section of link id 24589: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24589: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24589: 0.00053191184997559 --> \n<tr><td><a href=\"https:\/\/github.com\/arzwa\/wgd\" id=\"link-24098\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wgd<\/a>\n<!-- Time to render name section of link id 24098: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Python package and CLI for whole genome duplication analyse<\/p>\n<!-- Time to render link large description section of link id 24098: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_wgd> How to use <\/a>\n<!-- Time to render notes section of link id 24098: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24098: 0.0005490779876709 --> \n<tr><td><a href=\"https:\/\/github.com\/SunPengChuan\/wgdi\" id=\"link-25319\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WGDI<\/a>\n<!-- Time to render name section of link id 25319: 7.1525573730469E-6 --> \n<\/td>\n<td>WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments.\n<!-- Time to render link large description section of link id 25319: 1.1920928955078E-6 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WGDI> How to use <\/a>\n<!-- Time to render notes section of link id 25319: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25319: 0.00052499771118164 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/wgs-assembler\/\" id=\"link-24590\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WGS-Assembler<\/a>\n<!-- Time to render name section of link id 24590: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.<\/p>\n<!-- Time to render link large description section of link id 24590: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24590: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24590: 0.00049614906311035 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/wgsim\" id=\"link-24591\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Wgsim<\/a>\n<!-- Time to render name section of link id 24591: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Wgsim is a small tool for simulating sequence reads from a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24591: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24591: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24591: 0.00052309036254883 --> \n<tr><td><a href=\"https:\/\/github.com\/whatshap\/whatshap\/\" id=\"link-24592\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WhatsHap<\/a>\n<!-- Time to render name section of link id 24592: 6.9141387939453E-6 --> \n<\/td>\n<td><p>WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.<\/p>\n<!-- Time to render link large description section of link id 24592: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WhatsHap> How to use <\/a>\n<!-- Time to render notes section of link id 24592: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24592: 0.00051999092102051 --> \n<tr><td><a href=\"https:\/\/github.com\/timbitz\/Whippet.jl\" id=\"link-24593\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Whippet<\/a>\n<!-- Time to render name section of link id 24593: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Lightweight and Fast RNA-seq quantification at the event-level<\/p>\n<!-- Time to render link large description section of link id 24593: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24593: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24593: 0.00035405158996582 --> \n<tr><td><a href=\"https:\/\/github.com\/openai\/whisper\" id=\"link-25644\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Whisper<\/a>\n<!-- Time to render name section of link id 25644: 3.814697265625E-6 --> \n<\/td>\n<td><p>Whisper is a general-purpose speech recognition model. It is trained on a large dataset of diverse audio and is also a multitasking model that can perform multilingual speech recognition, speech translation, and language identification.<\/p>\n<!-- Time to render link large description section of link id 25644: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Whisper> How to use <\/a>\n<!-- Time to render notes section of link id 25644: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25644: 0.00022697448730469 --> \n<tr><td><a href=\"https:\/\/github.com\/LottePronk\/whokaryote\" id=\"link-24594\" class=\"track_this_link \" rel=\"noopener noreferrer\">whokaryote<\/a>\n<!-- Time to render name section of link id 24594: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Classification of metagenomic contigs as eukaryotic\/prokaryotic using biology-based features.<\/p>\n<!-- Time to render link large description section of link id 24594: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_whokaryote> How to use <\/a>\n<!-- Time to render notes section of link id 24594: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24594: 0.00022792816162109 --> \n<tr><td><a href=\"https:\/\/github.com\/Ensembl\/WiggleTools\" id=\"link-23982\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WiggleTools<\/a>\n<!-- Time to render name section of link id 23982: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc).<\/p>\n<!-- Time to render link large description section of link id 23982: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WiggleTools> How to use <\/a>\n<!-- Time to render notes section of link id 23982: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23982: 0.00023102760314941 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/Winnowmap\" id=\"link-24595\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Winnowmap<\/a>\n<!-- Time to render name section of link id 24595: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques.<\/p>\n<!-- Time to render link large description section of link id 24595: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24595: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24595: 0.00022792816162109 --> \n<tr><td><a href=\"https:\/\/github.com\/uym2\/wLogDate\" id=\"link-24596\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wLogDate<\/a>\n<!-- Time to render name section of link id 24596: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Molecular Dating using logarithmic penalty function. wLogDate is a method for dating phylogenetic trees. Given a phylogeny and either sampling times for leaves or calibration points for internal nodes, wLogDate outputs a \"dated\" tree that conforms to the sampling times or calibration points. It can also work with no sampling time or calibration points where it would simply turn the tree into ultrametric, fixing its height to a given value. Its optimization criterion is to minimize the variance of the mutation rates in log scale (hence the term logDate).<\/p>\n<!-- Time to render link large description section of link id 24596: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24596: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24596: 0.00023102760314941 --> \n<tr><td><a href=\"https:\/\/github.com\/fmaguire\/WoLFPSort\" id=\"link-25469\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WoLFPSort<\/a>\n<!-- Time to render name section of link id 25469: 2.8610229492188E-6 --> \n<\/td>\n<td><p>WoLF PSORT is an extension of the PSORT II program for protein subcellular localization prediction, which is based on the PSORT principle. WoLF PSORT converts a protein's amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs.<\/p>\n<!-- Time to render link large description section of link id 25469: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WoLFPSort> How to use <\/a>\n<!-- Time to render notes section of link id 25469: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25469: 0.00024700164794922 --> \n<tr><td><a href=\"https:\/\/github.com\/ruanjue\/wtdbg2\" id=\"link-23999\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wtdbg<\/a>\n<!-- Time to render name section of link id 23999: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT).<\/p>\n<!-- Time to render link large description section of link id 23999: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_wtdbg> How to use <\/a>\n<!-- Time to render notes section of link id 23999: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23999: 0.00023293495178223 --> \n<tr><td><a href=\"https:\/\/www.advbiocomp.com\/blast\/obsolete\/\" id=\"link-23763\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wu-blast<\/a>\n<!-- Time to render name section of link id 23763: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Similarity search against databanks, Washington University Blast.(OBSOLETE)<\/p>\n<!-- Time to render link large description section of link id 23763: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WuBlast> How to use <\/a>\n<!-- Time to render notes section of link id 23763: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23763: 0.00022506713867188 --> \n<tr><td><a href=\"https:\/\/github.com\/natir\/yacrd\" id=\"link-24100\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">yacrd<\/a>\n<!-- Time to render name section of link id 24100: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Yet Another Chimeric Read Detector for long reads<\/p>\n<!-- Time to render link large description section of link id 24100: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24100: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24100: 0.00022411346435547 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/yak\" id=\"link-24598\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Yak<\/a>\n<!-- Time to render name section of link id 24598: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Yak is initially developed for two specific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads.<\/p>\n<!-- Time to render link large description section of link id 24598: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24598: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24598: 0.00022506713867188 --> \n<tr><td><a href=\"https:\/\/github.com\/genid\/Yleaf\" id=\"link-24599\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Yleaf<\/a>\n<!-- Time to render name section of link id 24599: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software for human Y-chromosomal haplogroup inference from next generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24599: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Yleaf> How to use <\/a>\n<!-- Time to render notes section of link id 24599: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24599: 0.00022697448730469 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1164\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] 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[query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0022549629211426-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1164 level0\"><!-- Div Category --><div id=\"amplicon-analysis\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Amplicon analysis<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/pinellolab\/CRISPResso2\" id=\"link-25710\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRISPResso2<\/a>\n<!-- Time to render name section of link id 25710: 7.1525573730469E-6 --> \n<\/td>\n<td><p>CRISPResso is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Briefly, CRISPResso: aAligns sequencing reads to a reference sequence, quantifies insertions, mutations and deletions to determine whether a read is modified or unmodified by genome editing, summarizes editing results in intuitive plots and datasets.<\/p>\n<!-- Time to render link large description section of link id 25710: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CRISPResso2> How to use <\/a>\n<!-- Time to render notes section of link id 25710: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25710: 0.0003809928894043 --> \n<tr><td><a href=\"https:\/\/github.com\/USDA-ARS-GBRU\/itsxpress\" id=\"link-25732\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ITSxpress<\/a>\n<!-- Time to render name section of link id 25732: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis.<\/p>\n<!-- Time to render link large description section of link id 25732: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ITSxpress> How to use <\/a>\n<!-- Time to render notes section of link id 25732: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25732: 0.00035405158996582 --> \n<tr><td><a href=\"https:\/\/github.com\/envmetagen\/metabinkit\" id=\"link-25994\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">metabinkit<\/a>\n<!-- Time to render name section of link id 25994: 6.1988830566406E-6 --> \n<\/td>\n<td><p>From metagenomic or metabarcoding data, it is often necessary to assign taxonomy to DNA sequences. This is generally performed by aligning sequences to a reference database, usually resulting in multiple database alignments for each query sequence. Using these alignment results, metabinkit assigns a single taxon to each query sequence, based on user-defined percentage identity thresholds. In essence, for each query, the alignments are filtered based on the percentage identity thresholds and the lowest common ancestor for all alignments passing the filters is determined. The metabin program is not limited to BLAST alignments, and can accept alignment results produced using any program, provided the input format is correct. However, functionality is also available to create BLAST databases and to perform BLAST alignments, which can be passed directly to metabin.<\/p>\n<!-- Time to render link large description section of link id 25994: 3.0994415283203E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_metabinkit> How to use <\/a>\n<!-- Time to render notes section of link id 25994: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25994: 0.00035715103149414 --> \n<tr><td><a href=\"https:\/\/github.com\/noahares\/raxtax\" id=\"link-25810\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">raxtax<\/a>\n<!-- Time to render name section of link id 25810: 6.9141387939453E-6 --> \n<\/td>\n<td><p>raxtax is a fast and efficient k-mer-based non-Bayesian taxonomic classifier for barcoding DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 25810: 3.0994415283203E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_raxtax> How to use <\/a>\n<!-- Time to render notes section of link id 25810: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25810: 0.0003509521484375 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1126\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => 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2022-11-22 10:25:59\n            [post_date_gmt] => 2022-11-22 09:25:59\n            [post_content] => \n            [post_title] => AGAT\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => agat\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2025-05-21 07:22:29\n            [post_modified_gmt] => 2025-05-21 05:22:29\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/agat\/\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 152\n    [max_num_pages] => 0\n    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id=\"link-24135\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AGAT<\/a>\n<!-- Time to render name section of link id 24135: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Another Gff Analysis Toolkit: suite of tools to handle gene annotations in any GTF\/GFF format. Some examples what AGAT can do: standardise any GTF\/GFF file into a comprehensive GFF3 format (script with agat_sp prefix): add missing parent features (e.g. gene and mRNA if only CDS\/exon exist). add missing features (e.g. exon and UTR). add missing mandatory attributes (i.e. ID, Parent). fix identifier to be uniq. fix feature location. remove duplicated features. group related features (if spread in different places in the file). sort features. merge overlapping loci into one single locus (only if option activated).<\/p>\n<!-- Time to render link large description section of link id 24135: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AGAT> How to use <\/a>\n<!-- Time to render notes section of link id 24135: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24135: 0.00035381317138672 --> \n<tr><td><a href=\"https:\/\/lbgi.fr\/AnnotSV\/\" id=\"link-25353\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AnnotSV<\/a>\n<!-- Time to render name section of link id 25353: 5.9604644775391E-6 --> \n<\/td>\n<td><p>An integrated tool for Structural Variations annotation and ranking.<\/p>\n<!-- Time to render link large description section of link id 25353: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AnnotSV> How to use <\/a>\n<!-- Time to render notes section of link id 25353: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25353: 0.00035214424133301 --> \n<tr><td><a href=\"http:\/\/apoplastp.csiro.au\/index.html\" id=\"link-23903\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ApoplastP<\/a>\n<!-- Time to render name section of link id 23903: 5.9604644775391E-6 --> \n<\/td>\n<td><p>ApoplastP is a machine learning method for predicting localization of proteins to the plant apoplast. ApoplastP can distinguish non-apoplastic proteins from apoplastic proteins for both plant proteins and pathogen proteins. In particular, ApoplastP can predict if an effector localizes to the plant apoplast.<\/p>\n<!-- Time to render link large description section of link id 23903: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ApoplastP> How to use <\/a>\n<!-- Time to render notes section of link id 23903: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23903: 0.00032591819763184 --> \n<tr><td><a href=\"http:\/\/mbio-serv2.mbioekol.lu.se\/ARAGORN\/\" id=\"link-23587\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARAGORN<\/a>\n<!-- Time to render name section of link id 23587: 5.9604644775391E-6 --> \n<\/td>\n<td><p>ARAGORN is a program to detect tRNA genes and tmRNA genes in nucleotide sequence<\/p>\n<!-- Time to render link large description section of link id 23587: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23587: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23587: 0.00032305717468262 --> \n<tr><td><a href=\"http:\/\/bioinf.uni-greifswald.de\/augustus\/\" id=\"link-23588\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Augustus<\/a>\n<!-- Time to render name section of link id 23588: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Augustus is a program that predicts genes in eukaryotic genomic sequences<\/p>\n<!-- Time to render link large description section of link id 23588: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Augustus> How to use <\/a>\n<!-- Time to render notes section of link id 23588: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23588: 0.00029802322387695 --> \n<tr><td><a href=\"https:\/\/github.com\/GDKO\/AvP\" id=\"link-24708\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AvP<\/a>\n<!-- Time to render name section of link id 24708: 5.9604644775391E-6 --> \n<\/td>\n<td><p>AvP performs automatic detection of HGT candidates within a phylogenetic framework.<\/p>\n<!-- Time to render link large description section of link id 24708: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AvP> How to use <\/a>\n<!-- Time to render notes section of link id 24708: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24708: 0.00030016899108887 --> \n<tr><td><a href=\"https:\/\/github.com\/oschwengers\/bakta\" id=\"link-24151\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bakta<\/a>\n<!-- Time to render name section of link id 24151: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids.<\/p>\n<!-- Time to render link large description section of link id 24151: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bakta> How to use <\/a>\n<!-- Time to render notes section of link id 24151: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24151: 0.0003509521484375 --> \n<tr><td><a href=\"http:\/\/www.vicbioinformatics.com\/software.shtml\" id=\"link-23591\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Barrnap<\/a>\n<!-- Time to render name section of link id 23591: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).<\/p>\n<!-- Time to render link large description section of link id 23591: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23591: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23591: 0.00022196769714355 --> \n<tr><td><a href=\"https:\/\/developer.basespace.illumina.com\/docs\/content\/documentation\/cli\/cli-overview\" id=\"link-26129\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BaseSpace_CLI<\/a>\n<!-- Time to render name section of link id 26129: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Command line interface to work with BaseSpace Sequence Hub data.<\/p>\n<!-- Time to render link large description section of link id 26129: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BaseSpace_CLI> How to use <\/a>\n<!-- Time to render notes section of link id 26129: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26129: 0.00031781196594238 --> \n<tr><td><a href=\"http:\/\/bioinf.uni-greifswald.de\/bioinf\/braker\/index.html\" id=\"link-23782\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Braker<\/a>\n<!-- Time to render name section of link id 23782: 4.0531158447266E-6 --> \n<\/td>\n<td><p>BRAKER(1,2,3) is a tool for fully automated genome annotation with GeneMark-ET and AUGUSTUS<\/p>\n<!-- Time to render link large description section of link id 23782: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BRAKER> How to use <\/a>\n<!-- Time to render notes section of link id 23782: 2.1457672119141E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23782: 0.00022506713867188 --> \n<tr><td><a href=\"https:\/\/github.com\/EBI-Metagenomics\/emg-viral-pipeline\" id=\"link-25569\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAMISIM<\/a>\n<!-- Time to render name section of link id 25569: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CAMISIM is a software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets.<\/p>\n<!-- Time to render link large description section of link id 25569: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAMISIM> How to use <\/a\n<!-- Time to render notes section of link id 25569: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25569: 0.00022697448730469 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/Comparative-Annotation-Toolkit\" id=\"link-23985\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAT<\/a>\n<!-- Time to render name section of link id 23985: 5.0067901611328E-6 --> \n<\/td>\n<td><p>This project aims to provide a straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen.<\/p>\n<!-- Time to render link large description section of link id 23985: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23985: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23985: 0.00023913383483887 --> \n<tr><td><a href=\"http:\/\/korflab.ucdavis.edu\/datasets\/cegma\/\" id=\"link-23606\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CEGMA<\/a>\n<!-- Time to render name section of link id 23606: 4.0531158447266E-6 --> \n<\/td>\n<td><p>CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.<\/p>\n<!-- Time to render link large description section of link id 23606: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CEGMA> How to use <\/a>\n<!-- Time to render notes section of link id 23606: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23606: 0.00022602081298828 --> \n<tr><td><a href=\"http:\/\/www.girinst.org\/downloads\/software\/censor\/\" id=\"link-23853\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CENSOR<\/a>\n<!-- Time to render name section of link id 23853: 4.0531158447266E-6 --> \n<\/td>\n<td><p>CENSOR compares and masks protein or nucleotide sequences.<\/p>\n<!-- Time to render link large description section of link id 23853: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CENSOR> How to use <\/a>\n<!-- Time to render notes section of link id 23853: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23853: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/ernstlab.github.io\/ChromHMM\/\" id=\"link-25655\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ChromHMM<\/a>\n<!-- Time to render name section of link id 25655: 5.0067901611328E-6 --> \n<\/td>\n<td><p>ChromHMM is software for learning and characterizing chromatin states.<\/p>\n<!-- Time to render link large description section of link id 25655: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ChromHMM> How to use <\/a>\n<!-- Time to render notes section of link id 25655: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25655: 0.00035190582275391 --> \n<tr><td><a href=\"https:\/\/github.com\/YangLab\/CIRCexplorer2\" id=\"link-25068\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CIRCexplorer2<\/a>\n<!-- Time to render name section of link id 25068: 3.0994415283203E-6 --> \n<\/td>\n<td><p>CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset<\/p>\n<!-- Time to render link large description section of link id 25068: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CIRCexplorer2> How to use <\/a>\n<!-- Time to render notes section of link id 25068: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25068: 0.00024819374084473 --> \n<tr><td><a href=\"https:\/\/github.com\/martin-steinegger\/conterminator\" id=\"link-24800\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Conterminator<\/a>\n<!-- Time to render name section of link id 24800: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Conterminator is an efficient method for detecting incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison.<\/p>\n<!-- Time to render link large description section of link id 24800: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24800: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24800: 0.00019407272338867 --> \n<tr><td><a href=\"http:\/\/contra.stanford.edu\/contrast\/\" id=\"link-23987\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CONTRAST<\/a>\n<!-- Time to render name section of link id 23987: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CONTRAST predicts protein-coding genes from a multiple genomic alignment using a combination of discriminative machine learning techniques.<\/p>\n<!-- Time to render link large description section of link id 23987: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23987: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23987: 0.00020408630371094 --> \n<tr><td><a href=\"https:\/\/github.com\/linnabrown\/run_dbcan\/\" id=\"link-25604\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dbCAN3<\/a>\n<!-- Time to render name section of link id 25604: 3.0994415283203E-6 --> \n<\/td>\n<td><p>run_dbcan (dbCAN3) is the standalone version of the dbCAN3 annotation tool for automated CAZyme annotation.<\/p>\n<!-- Time to render link large description section of link id 25604: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dbCAN3> How to use <\/a>\n<!-- Time to render notes section of link id 25604: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25604: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/bbuchfink\/diamond\" id=\"link-23798\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIAMOND<\/a>\n<!-- Time to render name section of link id 23798: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Accelerated BLAST compatible local sequence aligner.<\/p>\n<!-- Time to render link large description section of link id 23798: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DIAMOND> How to use <\/a>\n<!-- Time to render notes section of link id 23798: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23798: 0.0001518726348877 --> \n<tr><td><a href=\"https:\/\/github.com\/rhysf\/DIAMOND2GO\" id=\"link-25540\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIAMOND2GO<\/a>\n<!-- Time to render name section of link id 25540: 3.0994415283203E-6 --> \n<\/td>\n<td>Diamond2GO is a set of tools that can rapidly assign gene ontology and perform enrichment for functional genomics.\n<!-- Time to render link large description section of link id 25540: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Diamond2GO> How to use <\/a>\n<!-- Time to render notes section of link id 25540: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25540: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/shafferm\/DRAM\" id=\"link-24202\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DRAM<\/a>\n<!-- Time to render name section of link id 24202: 5.9604644775391E-6 --> \n<\/td>\n<td><p>DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs.<\/p>\n<!-- Time to render link large description section of link id 24202: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24202: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24202: 0.00040793418884277 --> \n<tr><td><a href=\"https:\/\/github.com\/carnegie\/E2P2\" id=\"link-25295\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">E2P2<\/a>\n<!-- Time to render name section of link id 25295: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Ensemble Enzyme Prediction Pipeline.<\/p>\n<!-- Time to render link large description section of link id 25295: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_E2P2> How to use <\/a>\n<!-- Time to render notes section of link id 25295: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25295: 0.00026679039001465 --> \n<tr><td><a href=\"https:\/\/github.com\/oushujun\/EDTA\" id=\"link-24208\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EDTA<\/a>\n<!-- Time to render name section of link id 24208: 5.0067901611328E-6 --> \n<\/td>\n<td><p>This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.<\/p>\n<!-- Time to render link large description section of link id 24208: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EDTA> How to use <\/a>\n<!-- Time to render notes section of link id 24208: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24208: 0.00029706954956055 --> \n<tr><td><a href=\"https:\/\/github.com\/JanaSperschneider\/EffectorP-1.0\" id=\"link-25468\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EffectorP<\/a>\n<!-- Time to render name section of link id 25468: 5.0067901611328E-6 --> \n<\/td>\n<td><p>EffectorP is a machine learning method for fungal effector prediction in secretomes and has been trained to distinguish secreted proteins from secreted effectors in plant-pathogenic fungi.<\/p>\n<!-- Time to render link large description section of link id 25468: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EffectorP> How to use <\/a>\n<!-- Time to render notes section of link id 25468: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25468: 0.0002739429473877 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/egapx\" id=\"link-25748\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EGAPx<\/a>\n<!-- Time to render name section of link id 25748: 5.9604644775391E-6 --> \n<\/td>\n<td><p>EGAPx is the publicly accessible version of the updated NCBI Eukaryotic Genome Annotation Pipeline.<\/p>\n<!-- Time to render link large description section of link id 25748: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EGAPx> How to use <\/a>\n<!-- Time to render notes section of link id 25748: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25748: 0.00039100646972656 --> \n<tr><td><a href=\"https:\/\/github.com\/eggnogdb\/eggnog-mapper\" id=\"link-24209\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eggNog-mapper<\/a>\n<!-- Time to render name section of link id 24209: 5.0067901611328E-6 --> \n<\/td>\n<td><p>eggnog-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only.<\/p>\n<!-- Time to render link large description section of link id 24209: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eggNOG-mapper> How to use <\/a>\n<!-- Time to render notes section of link id 24209: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24209: 0.00026798248291016 --> \n<tr><td><a href=\"https:\/\/github.com\/google-deepmind\/deepmind-research\/tree\/master\/enformer\" id=\"link-26108\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Enformer<\/a>\n<!-- Time to render name section of link id 26108: 5.9604644775391E-6 --> \n<\/td>\n<td><p>This package provides an implementation of the Enformer model and examples on running the model.<\/p>\n<!-- Time to render link large description section of link id 26108: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Enformer> How to use <\/a>\n<!-- Time to render notes section of link id 26108: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26108: 0.00038981437683105 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/enTAP\/EnTAP\" id=\"link-24214\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EnTAP<\/a>\n<!-- Time to render name section of link id 24214: 5.9604644775391E-6 --> \n<\/td>\n<td><p>EnTAP is an eukaryotic non-model annotation pipeline developed by Alexander Hart and Dr. Jill Wegrzyn of the Plant Computational Genomics Lab at the University of Connecticut.<\/p>\n<!-- Time to render link large description section of link id 24214: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24214: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24214: 0.00042080879211426 --> \n<tr><td><a href=\"http:\/\/eugene.toulouse.inra.fr\/\" id=\"link-24217\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EuGeneEP<\/a>\n<!-- Time to render name section of link id 24217: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EuGene is an open integrative gene finder for eukaryotic and prokaryotic genomes. EuGene-EP (Eukaryote Pipeline) facilitates the application of EuGene on eukaryote genomes.<\/p>\n<!-- Time to render link large description section of link id 24217: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24217: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24217: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/evidencemodeler.github.io\/\" id=\"link-23848\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EVidenceModeler (EVM)<\/a>\n<!-- Time to render name section of link id 23848: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.<\/p>\n<!-- Time to render link large description section of link id 23848: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EVidenceModeler> How to use <\/a>\n<!-- Time to render notes section of link id 23848: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23848: 0.00015592575073242 --> \n<tr><td><a href=\"https:\/\/github.com\/sagnikbanerjee15\/Finder\" id=\"link-24233\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Finder<\/a>\n<!-- Time to render name section of link id 24233: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Finder is a gene annotator pipeline which automates the process of downloading short reads, aligning them and using the assembled transcripts to generate gene annotations.<\/p>\n<!-- Time to render link large description section of link id 24233: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24233: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24233: 0.00024890899658203 --> \n<tr><td><a href=\"https:\/\/github.com\/schneebergerlab\/fixchr\" id=\"link-24970\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fixchr<\/a>\n<!-- Time to render name section of link id 24970: 4.0531158447266E-6 --> \n<\/td>\n<td><p>This package selects homologous chromosomes between two genomes by comparing whole-genome alignments between them. Additionally, it generates dotplots for quick checking of the output.<\/p>\n<!-- Time to render link large description section of link id 24970: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fixchr> How to use <\/a>\n<!-- Time to render notes section of link id 24970: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24970: 0.00023698806762695 --> \n<tr><td><a href=\"https:\/\/github.com\/tolkit\/fpma\" id=\"link-24238\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fpma<\/a>\n<!-- Time to render name section of link id 24238: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Fast Plant Mito Annotation.<\/p>\n<!-- Time to render link large description section of link id 24238: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24238: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24238: 0.00023198127746582 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/fraggenescan\/\" id=\"link-23937\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FragGeneScan<\/a>\n<!-- Time to render name section of link id 23937: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.<\/p>\n<!-- Time to render link large description section of link id 23937: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23937: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23937: 0.00016093254089355 --> \n<tr><td><a href=\"https:\/\/github.com\/unipept\/FragGeneScanRs\" id=\"link-25302\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FragGeneScanRs<\/a>\n<!-- Time to render name section of link id 25302: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FragGeneScanRs is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.<\/p>\r\n<p>It is a re-implementation of FragGeneScan in Rust.<\/p>\n<!-- Time to render link large description section of link id 25302: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FragGeneScanRs> How to use <\/a>\n<!-- Time to render notes section of link id 25302: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25302: 0.0001530647277832 --> \n<tr><td><a href=\"https:\/\/iant.toulouse.inra.fr\/\/FrameDP\/\" id=\"link-23631\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FrameDP<\/a>\n<!-- Time to render name section of link id 23631: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Sensitive peptide detection on noisy matured sequences. Available with command line interface on the cluster.<\/p>\n<!-- Time to render link large description section of link id 23631: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23631: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23631: 0.00015115737915039 --> \n<tr><td><a href=\"https:\/\/funannotate.readthedocs.io\/en\/latest\/index.html\" id=\"link-24241\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Funannotate<\/a>\n<!-- Time to render name section of link id 24241: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Funannotate is a genome prediction, annotation, and comparison software package.<\/p>\n<!-- Time to render link large description section of link id 24241: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Funannotate> How to use <\/a>\n<!-- Time to render notes section of link id 24241: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24241: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/github.com\/NBISweden\/GAAS\" id=\"link-24242\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GAAS<\/a>\n<!-- Time to render name section of link id 24242: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Genome Assembly Annotation Service: Suite of tools related to Genome Assembly Annotation Service tasks.<\/p>\n<!-- Time to render link large description section of link id 24242: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24242: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24242: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/GALBA\" id=\"link-24602\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GALBA<\/a>\n<!-- Time to render name section of link id 24602: 2.8610229492188E-6 --> \n<\/td>\n<td><p>GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available.<\/p>\n<!-- Time to render link large description section of link id 24602: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24602: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24602: 0.00015401840209961 --> \n<tr><td><a href=\"http:\/\/www.jstacs.de\/index.php\/GeMoMa\" id=\"link-24244\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeMoMa<\/a>\n<!-- Time to render name section of link id 24244: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Gene Model Mapper (GeMoMa) is a homology-based gene prediction program.<\/p>\n<!-- Time to render link large description section of link id 24244: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24244: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24244: 0.00015902519226074 --> \n<tr><td><a href=\"http:\/\/genome.crg.es\/software\/geneid\/\" id=\"link-23950\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">geneid<\/a>\n<!-- Time to render name section of link id 23950: 3.0994415283203E-6 --> \n<\/td>\n<td><p>geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.<\/p>\n<!-- Time to render link large description section of link id 23950: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_geneid> How to use <\/a>\n<!-- Time to render notes section of link id 23950: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23950: 0.00014996528625488 --> \n<tr><td><a href=\"http:\/\/opal.biology.gatech.edu\/GeneMark\/\" id=\"link-23863\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneMark-ES<\/a>\n<!-- Time to render name section of link id 23863: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Unsupervised training is an important feature of the GeneMark-ES algorithm that identifies protein coding genes in eukaryotic genomes. This is the only eukaryotic gene finder that can perform gene prediction without curated training sets.<\/p>\n<!-- Time to render link large description section of link id 23863: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GeneMark> How to use <\/a>\n<!-- Time to render notes section of link id 23863: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23863: 0.00014996528625488 --> \n<tr><td><a href=\"http:\/\/opal.biology.gatech.edu\/GeneMark\/\" id=\"link-23636\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneMark-ET<\/a>\n<!-- Time to render name section of link id 23636: 3.0994415283203E-6 --> \n<\/td>\n<td><p>a semi-supervised version of GeneMark-ES, called GeneMark-ET that uses RNA-Seq reads to improve training.<\/p>\n<!-- Time to render link large description section of link id 23636: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GeneMark> How to use <\/a>\n<!-- Time to render notes section of link id 23636: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23636: 0.00015497207641602 --> \n<tr><td><a href=\"https:\/\/github.com\/gatech-genemark\/GeneMark-ETP\" id=\"link-24690\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneMark-ETP<\/a>\n<!-- Time to render name section of link id 24690: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Gene finding in eukaryotic genomes supported by transcriptome sequencing and protein homology.<\/p>\n<!-- Time to render link large description section of link id 24690: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GeneMark-ETP> How to use <\/a>\n<!-- Time to render notes section of link id 24690: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24690: 0.00023889541625977 --> \n<tr><td><a href=\"http:\/\/exon.gatech.edu\/GeneMark\/\" id=\"link-24245\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneMarkS<\/a>\n<!-- Time to render name section of link id 24245: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.<\/p>\n<!-- Time to render link large description section of link id 24245: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GeneMarkS-T> How to use <\/a>\n<!-- Time to render notes section of link id 24245: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24245: 0.00024795532226562 --> \n<tr><td><a href=\"https:\/\/github.com\/cpockrandt\/genmap\" id=\"link-25923\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenMap<\/a>\n<!-- Time to render name section of link id 25923: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast and Exact Computation of Genome Mappability.<\/p>\n<!-- Time to render link large description section of link id 25923: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenMap> How to use <\/a>\n<!-- Time to render notes section of link id 25923: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25923: 0.00013494491577148 --> \n<tr><td><a href=\"http:\/\/genomethreader.org\/\" id=\"link-23887\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeThreader<\/a>\n<!-- Time to render name section of link id 23887: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA\/EST and\/or protein sequences are used to predict gene structures via spliced alignments.<\/p>\n<!-- Time to render link large description section of link id 23887: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeThreader> How to use <\/a>\n<!-- Time to render notes section of link id 23887: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23887: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-pathogens\/gff3toembl\" id=\"link-23929\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gff3toembl<\/a>\n<!-- Time to render name section of link id 23929: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI<\/p>\n<!-- Time to render link large description section of link id 23929: 7.1525573730469E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23929: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23929: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/bacpop\/ggCaller\" id=\"link-25574\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ggCaller<\/a>\n<!-- Time to render name section of link id 25574: 1.9073486328125E-6 --> \n<\/td>\n<td>A de Bruijn graph-based gene-caller and pangenome analysis tool.\n<!-- Time to render link large description section of link id 25574: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ggCaller> How to use <\/a>\n<!-- Time to render notes section of link id 25574: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25574: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/i10labtitech\/GINGER\" id=\"link-25803\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GINGER<\/a>\n<!-- Time to render name section of link id 25803: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GINGER is a tool that is implemented an integrated method for gene structure prediction in higher eukaryotes.<\/p>\n<!-- Time to render link large description section of link id 25803: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GINGER> How to use <\/a>\n<!-- Time to render notes section of link id 25803: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25803: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/ccb.jhu.edu\/software\/glimmerhmm\/\" id=\"link-25512\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GlimmerHMM<\/a>\n<!-- Time to render name section of link id 25512: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).<\/p>\n<!-- Time to render link large description section of link id 25512: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GlimmerHMM> How to use <\/a>\n<!-- Time to render notes section of link id 25512: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25512: 0.00011014938354492 --> \n<tr><td><a href=\"http:\/\/www.genoscope.cns.fr\/externe\/gmove\/\" id=\"link-23800\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gmove<\/a>\n<!-- Time to render name section of link id 23800: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Gmove is a genome annotation tool. This combiner takes as input mapping of RNA-seq or protein or ab initio data.<\/p>\n<!-- Time to render link large description section of link id 23800: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23800: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23800: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/cgroza\/GraffiTE\" id=\"link-25334\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraffiTE<\/a>\n<!-- Time to render name section of link id 25334: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and\/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.<\/p>\n<!-- Time to render link large description section of link id 25334: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GraffiTE> How to use <\/a>\n<!-- Time to render notes section of link id 25334: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25334: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/forge.ird.fr\/diade\/dynadiv\/grannot\" id=\"link-25728\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GrAnnoT<\/a>\n<!-- Time to render name section of link id 25728: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GrAnnoT is an annotation transfer tool for pangenome graphs.<\/p>\n<!-- Time to render link large description section of link id 25728: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GrAnnoT> How to use <\/a>\n<!-- Time to render notes section of link id 25728: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25728: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/GUSHR\" id=\"link-24269\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GUSHR<\/a>\n<!-- Time to render name section of link id 24269: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation. This tool has been adapted to the format needs of AUGUSTUS\/BRAKER and employs GeMoMa for generating UTRs from RNA-Seq coverage data.<\/p>\n<!-- Time to render link large description section of link id 24269: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GUSHR> How to use <\/a>\n<!-- Time to render notes section of link id 24269: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24269: 0.00052690505981445 --> \n<tr><td><a href=\"https:\/\/github.com\/HMPNK\/HANNO\" id=\"link-25535\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HANNO<\/a>\n<!-- Time to render name section of link id 25535: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Efficient High-throughput ANNOtation of protein coding genes in eukaryote genomes.<\/p>\n<!-- Time to render link large description section of link id 25535: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HANNO> How to use <\/a>\n<!-- Time to render notes section of link id 25535: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25535: 0.00034880638122559 --> \n<tr><td><a href=\"https:\/\/github.com\/weberlab-hhu\/Helixer\" id=\"link-24868\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Helixer<\/a>\n<!-- Time to render name section of link id 24868: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Using Deep Learning to predict gene annotations.<\/p>\n<!-- Time to render link large description section of link id 24868: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Helixer> How to use <\/a>\n<!-- Time to render notes section of link id 24868: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24868: 0.00050806999206543 --> \n<tr><td><a href=\"https:\/\/github.com\/TonyBolger\/HelixerPost\" id=\"link-24956\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HelixerPost<\/a>\n<!-- Time to render name section of link id 24956: 7.1525573730469E-6 --> \n<\/td>\n<td><p>HelixerPost uses a sliding window assessment to determine regions of the genome which are likely gene containing.<\/p>\n<!-- Time to render link large description section of link id 24956: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HelixerPost> How to use <\/a>\n<!-- Time to render notes section of link id 24956: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24956: 0.0005030632019043 --> \n<tr><td><a href=\"https:\/\/github.com\/richarddurbin\/hexamer\" id=\"link-25443\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hexamer<\/a>\n<!-- Time to render name section of link id 25443: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Find likely coding segments in DNA using composition-normalised hexamer tables.<\/p>\n<!-- Time to render link large description section of link id 25443: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hexamer> How to use <\/a>\n<!-- Time to render notes section of link id 25443: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25443: 0.00032305717468262 --> \n<tr><td><a href=\"https:\/\/icescreen.migale.inrae.fr\" id=\"link-25280\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ICEscreen<\/a>\n<!-- Time to render name section of link id 25280: 5.0067901611328E-6 --> \n<\/td>\n<td><p>ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes.<\/p>\n<!-- Time to render link large description section of link id 25280: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ICEscreen> How to use <\/a>\n<!-- Time to render notes section of link id 25280: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25280: 0.00026202201843262 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/infernal\/\" id=\"link-23648\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Infernal<\/a>\n<!-- Time to render name section of link id 23648: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).<\/p>\n<!-- Time to render link large description section of link id 23648: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Infernal> How to use <\/a>\n<!-- Time to render notes section of link id 23648: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23648: 0.0002748966217041 --> \n<tr><td><a href=\"https:\/\/github.com\/gem-pasteur\/Integron_Finder\" id=\"link-24302\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Integron Finder<\/a>\n<!-- Time to render name section of link id 24302: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Bioinformatics tool to find integrons in bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 24302: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Integron_Finder> How to use <\/a>\n<!-- Time to render notes section of link id 24302: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24302: 0.00039005279541016 --> \n<tr><td><a href=\"https:\/\/github.com\/genemine\/iread\" id=\"link-24324\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iREAD<\/a>\n<!-- Time to render name section of link id 24324: 5.0067901611328E-6 --> \n<\/td>\n<td><p>iREAD (intron REtention Analysis and Detector)is a tool to detect intron retention(IR) events from RNA-seq datasets.<\/p>\n<!-- Time to render link large description section of link id 24324: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24324: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24324: 0.00026893615722656 --> \n<tr><td><a href=\"https:\/\/github.com\/xiezhq\/ISEScan\" id=\"link-26177\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ISEScan<\/a>\n<!-- Time to render name section of link id 26177: 5.0067901611328E-6 --> \n<\/td>\n<td><p>A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome.<\/p>\r\n<p>ISEScan can be used to identify\/annotate full-length or non-full-length IS elements in any DNA sequence but ISEScan was only tested on prokarytoic genome including draft genome and meta-genome.<\/p>\r\n<p>Among the existing tools identifying IS elements, ISEScan might be the only one that gives TIR (Terminal Inverted Repeat) sequences.<\/p>\n<!-- Time to render link large description section of link id 26177: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ISEScan> How to use <\/a>\n<!-- Time to render notes section of link id 26177: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26177: 0.0002748966217041 --> \n<tr><td><a href=\"https:\/\/github.com\/takaram\/kofam_scan\" id=\"link-24839\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KofamScan<\/a>\n<!-- Time to render name section of link id 24839: 5.0067901611328E-6 --> \n<\/td>\n<td><p>KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model<\/p>\n<!-- Time to render link large description section of link id 24839: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KofamScan> How to use <\/a>\n<!-- Time to render notes section of link id 24839: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24839: 0.00026679039001465 --> \n<tr><td><a href=\"https:\/\/github.com\/agshumate\/Liftoff\" id=\"link-24346\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Liftoff<\/a>\n<!-- Time to render name section of link id 24346: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.<\/p>\n<!-- Time to render link large description section of link id 24346: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Liftoff> How to use <\/a>\n<!-- Time to render notes section of link id 24346: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24346: 0.00028014183044434 --> \n<tr><td><a href=\"https:\/\/ccb.jhu.edu\/lifton\/index.html\" id=\"link-25503\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LiftOn<\/a>\n<!-- Time to render name section of link id 25503: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Accurate annotation mapping for GFF\/GTF across assemblies.<\/p>\n<!-- Time to render link large description section of link id 25503: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LiftOn> How to use <\/a>\n<!-- Time to render notes section of link id 25503: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25503: 0.00041103363037109 --> \n<tr><td><a href=\"https:\/\/github.com\/JanaSperschneider\/LOCALIZER\" id=\"link-25471\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LOCALIZER<\/a>\n<!-- Time to render name section of link id 25471: 5.0067901611328E-6 --> \n<\/td>\n<td><p>LOCALIZER is a machine learning method for predicting the subcellular localization of both plant proteins and pathogen effectors in the plant cell.<\/p>\n<!-- Time to render link large description section of link id 25471: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LOCALIZER> How to use <\/a>\n<!-- Time to render notes section of link id 25471: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25471: 0.00027608871459961 --> \n<tr><td><a href=\"https:\/\/github.com\/Rostlab\/LocTree3\" id=\"link-23796\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Loctree3<\/a>\n<!-- Time to render name section of link id 23796: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Protein Subcelullar Localization Sequenced-Based Predictor<\/p>\n<!-- Time to render link large description section of link id 23796: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LocTree> How to use <\/a>\n<!-- Time to render notes section of link id 23796: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23796: 0.00025820732116699 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/longdust\" id=\"link-26089\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">longdust<\/a>\n<!-- Time to render name section of link id 26089: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Longdust identifies long highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs) in a genome.<\/p>\n<!-- Time to render link large description section of link id 26089: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_longdust> How to use <\/a>\n<!-- Time to render notes section of link id 26089: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26089: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/BioinformaticsToolsmith\/Look4TRs\" id=\"link-25164\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Look4TRs<\/a>\n<!-- Time to render name section of link id 25164: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A de-novo tool for detecting simple tandem repeats using self-supervised hidden Markov models.<\/p>\n<!-- Time to render link large description section of link id 25164: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Look4TRs> How to use <\/a>\n<!-- Time to render notes section of link id 25164: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25164: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/oushujun\/LTR_FINDER_parallel\" id=\"link-24359\" class=\"track_this_link \" rel=\"noopener noreferrer\">LTR_FINDER_parallel<\/a>\n<!-- Time to render name section of link id 24359: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A parallel wrapper for LTR_FINDER (LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.)<\/p>\n<!-- Time to render link large description section of link id 24359: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24359: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24359: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/github.com\/oushujun\/LTR_retriever\" id=\"link-24856\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LTR_retriever<\/a>\n<!-- Time to render name section of link id 24856: 1.9073486328125E-6 --> \n<\/td>\n<td><p>LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons.<\/p>\n<!-- Time to render link large description section of link id 24856: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LTR_retriever> How to use <\/a>\n<!-- Time to render notes section of link id 24856: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24856: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/gem-pasteur\/macsyfinder\/\" id=\"link-26122\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MacSyFinder<\/a>\n<!-- Time to render name section of link id 26122: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Detection of macromolecular systems in protein datasets using systems modelling and similarity search.<\/p>\r\n<p>Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system.\u00a0<\/p>\n<!-- Time to render link large description section of link id 26122: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MacSyFinder> How to use <\/a>\n<!-- Time to render notes section of link id 26122: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26122: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/www.yandell-lab.org\/software\/maker.html\" id=\"link-24064\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAKER<\/a>\n<!-- Time to render name section of link id 24064: 1.2874603271484E-5 --> \n<\/td>\n<td><p>MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.<\/p>\n<!-- Time to render link large description section of link id 24064: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAKER> How to use <\/a>\n<!-- Time to render notes section of link id 24064: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24064: 0.0001227855682373 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/metaeuk\" id=\"link-24375\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaEuk<\/a>\n<!-- Time to render name section of link id 24375: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.<\/p>\n<!-- Time to render link large description section of link id 24375: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaEuk> How to use <\/a>\n<!-- Time to render notes section of link id 24375: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24375: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/BFL-lab\/Mfannot\" id=\"link-24380\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mfannot<\/a>\n<!-- Time to render name section of link id 24380: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.<\/p>\n<!-- Time to render link large description section of link id 24380: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24380: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24380: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/caleblareau\/mgatk\" id=\"link-25397\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mgatk<\/a>\n<!-- Time to render name section of link id 25397: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A mitochondrial genome analysis toolkit.<\/p>\n<!-- Time to render link large description section of link id 25397: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mgatk> How to use <\/a>\n<!-- Time to render notes section of link id 25397: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25397: 0.00012302398681641 --> \n<tr><td><a href=\"https:\/\/github.com\/ctSkennerton\/minced\/\" id=\"link-23666\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MinCED<\/a>\n<!-- Time to render name section of link id 23666: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the command-line and was derived from CRT<\/p>\n<!-- Time to render link large description section of link id 23666: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23666: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23666: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/RemiAllio\/MitoFinder\" id=\"link-24388\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoFinder<\/a>\n<!-- Time to render name section of link id 24388: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data. MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi\/PacBio\/Nanopore\/Illumina sequencing data...)<\/p>\n<!-- Time to render link large description section of link id 24388: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24388: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24388: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/dpuiu\/MitoHPC\" id=\"link-25224\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoHPC<\/a>\n<!-- Time to render name section of link id 25224: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MitoHPC : Mitochondrial High Performance Caller. For Calling Mitochondrial Homoplasmies and Heteroplasmies.<\/p>\n<!-- Time to render link large description section of link id 25224: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoHPC> How to use <\/a>\n<!-- Time to render notes section of link id 25224: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25224: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/riverlee\/MitoSeek\" id=\"link-24390\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoSeek<\/a>\n<!-- Time to render name section of link id 24390: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.<\/p>\n<!-- Time to render link large description section of link id 24390: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24390: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24390: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/linzhi2013\/MitoZ\" id=\"link-24392\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoZ<\/a>\n<!-- Time to render name section of link id 24392: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization.<\/p>\n<!-- Time to render link large description section of link id 24392: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoZ> How to use <\/a>\n<!-- Time to render notes section of link id 24392: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24392: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/milaboratory\/mixcr\" id=\"link-24393\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiXCR<\/a>\n<!-- Time to render name section of link id 24393: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24393: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24393: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24393: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/phac-nml\/mob-suite\" id=\"link-26168\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MOB-suite<\/a>\n<!-- Time to render name section of link id 26168: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.<\/p>\r\n<p>The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.<\/p>\n<!-- Time to render link large description section of link id 26168: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MOB-suite> How to use <\/a>\n<!-- Time to render notes section of link id 26168: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26168: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/mhkj\/mge_finder\" id=\"link-24396\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MobileElementFinder<\/a>\n<!-- Time to render name section of link id 24396: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MobileElementFinder is a tool for identifying Mobile Genetic Elements (MGEs) in Whole Genome Shotgun sequence data.<\/p>\n<!-- Time to render link large description section of link id 24396: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MobileElementFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24396: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24396: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/xjtu-omics\/msisensor-pro\" id=\"link-25252\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MSIsensor-pro<\/a>\n<!-- Time to render name section of link id 25252: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25252: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MSIsensor-pro> How to use <\/a>\n<!-- Time to render notes section of link id 25252: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25252: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/steuernb\/NLR-Annotator\" id=\"link-24417\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NLR-Annotator<\/a>\n<!-- Time to render name section of link id 24417: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. NLR-Annotator is a tool to annotate loci associated with NLRs in large sequences.<\/p>\n<!-- Time to render link large description section of link id 24417: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24417: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24417: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/slt666666\/NLRtracker\" id=\"link-25307\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NLRtracker<\/a>\n<!-- Time to render name section of link id 25307: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NLRtracker extracts and functionally annotates NLRs from protein or transcript files based on the core features found in the RefPlantNLR dataset.<\/p>\n<!-- Time to render link large description section of link id 25307: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NLRtracker> How to use <\/a>\n<!-- Time to render notes section of link id 25307: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25307: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/pseudogene\/ora\" id=\"link-23959\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ORA<\/a>\n<!-- Time to render name section of link id 23959: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 40kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functional with DNA and EST sequence, no intron supported.<\/p>\n<!-- Time to render link large description section of link id 23959: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23959: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23959: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/orffinder\/\" id=\"link-24427\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ORFfinder<\/a>\n<!-- Time to render name section of link id 24427: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ORFfinder searches for open reading frames (ORFs) in the DNA sequence you enter.<\/p>\n<!-- Time to render link large description section of link id 24427: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ORFfinder> How to use <\/a>\n<!-- Time to render notes section of link id 24427: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24427: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/urmi-21\/orfipy\" id=\"link-24428\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">orfipy<\/a>\n<!-- Time to render name section of link id 24428: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Fast and flexible ORF finder.<\/p>\n<!-- Time to render link large description section of link id 24428: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24428: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24428: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/davidemms\/OrthoFinder\" id=\"link-23920\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OrthoFinder<\/a>\n<!-- Time to render name section of link id 23920: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.<\/p>\n<!-- Time to render link large description section of link id 23920: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OrthoFinder> How to use <\/a>\n<!-- Time to render notes section of link id 23920: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23920: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/rcedgar\/palm_annot\" id=\"link-25761\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">palm_annot<\/a>\n<!-- Time to render name section of link id 25761: 1.9073486328125E-6 --> \n<\/td>\n<td>Scripts, HMMs and search databases for identifying and classifying viral RdRp sequences \n<!-- Time to render link large description section of link id 25761: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_palm_annot> How to use <\/a>\n<!-- Time to render notes section of link id 25761: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25761: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/rcedgar\/palmscan\" id=\"link-25921\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Palmscan<\/a>\n<!-- Time to render name section of link id 25921: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Palmscan is software to detect viral polymerase palmprint barcode sequences in longer sequences such as virus genomes and ORFs. Palmprints can be used to classify RNA viruses.<\/p>\n<!-- Time to render link large description section of link id 25921: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Palmscan> How to use <\/a>\n<!-- Time to render notes section of link id 25921: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25921: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/gem-pasteur\/PanACoTA\" id=\"link-26201\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanACoTA<\/a>\n<!-- Time to render name section of link id 26201: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PANgenome with Annotations, COre identification, Tree and corresponding Alignments.<\/p>\n<!-- Time to render link large description section of link id 26201: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanACoTA> How to use <\/a>\n<!-- Time to render notes section of link id 26201: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26201: 0.00012779235839844 --> \n<tr><td><a href=\"https:\/\/pantools.readthedocs.io\/en\/latest\/\" id=\"link-25000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanTools<\/a>\n<!-- Time to render name section of link id 25000: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PanTools is a toolkit for comparative analysis of large number of genomes.<\/p>\n<!-- Time to render link large description section of link id 25000: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanTools> How to use <\/a>\n<!-- Time to render notes section of link id 25000: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25000: 0.00012683868408203 --> \n<tr><td><a href=\"https:\/\/github.com\/PASApipeline\/PASApipeline\" id=\"link-23687\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PASApipeline<\/a>\n<!-- Time to render name section of link id 23687: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.<\/p>\n<!-- Time to render link large description section of link id 23687: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PASApipeline> How to use <\/a>\n<!-- Time to render notes section of link id 23687: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23687: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/git-r3lab.uni.lu\/laura.denies\/PathoFact\" id=\"link-24434\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PathoFact<\/a>\n<!-- Time to render name section of link id 24434: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance.<\/p>\n<!-- Time to render link large description section of link id 24434: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24434: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24434: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/haessar\/peaks2utr\" id=\"link-26088\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">peaks2utr<\/a>\n<!-- Time to render name section of link id 26088: 2.1457672119141E-6 --> \n<\/td>\n<td><p>peaks2utr is a Python command-line tool that annotates 3' untranslated regions (UTR) for a given set of aligned sequencing reads in BAM format, and canonical annotation in GFF or GTF format.<\/p>\n<!-- Time to render link large description section of link id 26088: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_peaks2utr> How to use <\/a>\n<!-- Time to render notes section of link id 26088: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26088: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/pgap\" id=\"link-24438\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PGAP<\/a>\n<!-- Time to render name section of link id 24438: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).<\/p>\n<!-- Time to render link large description section of link id 24438: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pgap> How to use <\/a>\n<!-- Time to render notes section of link id 24438: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24438: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/boulund\/phaster_scripts\" id=\"link-25290\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHASTER_scripts<\/a>\n<!-- Time to render name section of link id 25290: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Small utility scripts to query the PHASTER API endpoint, to identify and annotate prophage sequences within bacterial genomes and plasmids.<\/p>\n<!-- Time to render link large description section of link id 25290: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHASTER_scripts> How to use <\/a>\n<!-- Time to render notes section of link id 25290: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25290: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/linsalrob\/PhiSpy\" id=\"link-24441\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhiSpy<\/a>\n<!-- Time to render name section of link id 24441: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.<\/p>\n<!-- Time to render link large description section of link id 24441: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24441: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24441: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/phobius.sbc.su.se\/index.html\" id=\"link-23956\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Phobius<\/a>\n<!-- Time to render name section of link id 23956: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A combined transmembrane topology and signal peptide predictor.<\/p>\n<!-- Time to render link large description section of link id 23956: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23956: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23956: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/plantismash\/plantismash\" id=\"link-25929\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlantiSMASH<\/a>\n<!-- Time to render name section of link id 25929: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PlantiSMASH is a specialized extension of antiSMASH for the identification and analysis of biosynthetic gene clusters (BGCs) in plant genomes. It supports advanced plant-specific detection rules and features for comparative genomics, visualization, and more.<\/p>\n<!-- Time to render link large description section of link id 25929: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlantiSMASH> How to use <\/a>\n<!-- Time to render notes section of link id 25929: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25929: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/smaegol\/PlasFlow\" id=\"link-24776\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlasFlow<\/a>\n<!-- Time to render name section of link id 24776: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software for prediction of plasmid sequences in metagenomic assemblies.<\/p>\n<!-- Time to render link large description section of link id 24776: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlasFlow> How to use <\/a>\n<!-- Time to render notes section of link id 24776: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24776: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/plasmidfinder\" id=\"link-24452\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlasmidFinder<\/a>\n<!-- Time to render name section of link id 24452: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The service identifies plasmids in total or partial sequenced isolates of bacteria.<\/p>\n<!-- Time to render link large description section of link id 24452: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlasmidFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24452: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24452: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/portcullis.readthedocs.io\/en\/latest\/\" id=\"link-23986\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Portcullis<\/a>\n<!-- Time to render name section of link id 23986: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Splice junction analysis and filtering from BAM files.<\/p>\n<!-- Time to render link large description section of link id 23986: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23986: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23986: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/BolognaBiocomp\/predgpi\" id=\"link-25470\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PredGPI<\/a>\n<!-- Time to render name section of link id 25470: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Prediction of glycosylphosphatidylinositol-anchors in proteins based on HMMs and SVMs.<\/p>\n<!-- Time to render link large description section of link id 25470: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PredGPI> How to use <\/a>\n<!-- Time to render notes section of link id 25470: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25470: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/prodigal.ornl.gov\/\" id=\"link-23700\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Prodigal<\/a>\n<!-- Time to render name section of link id 23700: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Prodigal (<b>Pro<\/b>karyotic <b>Dy<\/b>namic Programming <b>G<\/b>enefinding <b>Al<\/b>gorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.<\/p>\n<!-- Time to render link large description section of link id 23700: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Prodigal> How to use <\/a>\n<!-- Time to render notes section of link id 23700: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23700: 0.00013899803161621 --> \n<tr><td><a href=\"https:\/\/github.com\/tseemann\/prokka\" id=\"link-23701\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROKKA<\/a>\n<!-- Time to render name section of link id 23701: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank\/DDJB\/ENA.<\/p>\n<!-- Time to render link large description section of link id 23701: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PROKKA> How to use <\/a>\n<!-- Time to render notes section of link id 23701: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23701: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/salzberg-lab\/PSAURON\" id=\"link-25414\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PSAURON<\/a>\n<!-- Time to render name section of link id 25414: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PSAURON is a machine learning model for rapid assessment of protein coding gene annotation.<\/p>\n<!-- Time to render link large description section of link id 25414: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PSAURON> How to use <\/a>\n<!-- Time to render notes section of link id 25414: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25414: 0.00012302398681641 --> \n<tr><td><a href=\"https:\/\/github.com\/filip-husnik\/pseudofinder\" id=\"link-25019\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pseudofinder<\/a>\n<!-- Time to render name section of link id 25019: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Detection of pseudogene candidates in bacterial and archaeal genomes.<\/p>\n<!-- Time to render link large description section of link id 25019: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 25019: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25019: 0.00012087821960449 --> \n<tr><td><a href=\"https:\/\/github.com\/RabbitBio\/RabbitV\" id=\"link-24480\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RabbitV<\/a>\n<!-- Time to render name section of link id 24480: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RabbitV is a highly optimized and practical toolkit for the detection of viruses and microorganisms in sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24480: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24480: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24480: 0.00011897087097168 --> \n<tr><td><a href=\"http:\/\/ratt.sourceforge.net\/index.html\" id=\"link-23884\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RATT<\/a>\n<!-- Time to render name section of link id 23884: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.<\/p>\n<!-- Time to render link large description section of link id 23884: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23884: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23884: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/dimitris-karapliafis\/RdRpCATCH\" id=\"link-25763\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RdRpCATCH<\/a>\n<!-- Time to render name section of link id 25763: 2.8610229492188E-6 --> \n<\/td>\n<td>A community effort to create a shared resource for HMM-based RdRp discovery \n<!-- Time to render link large description section of link id 25763: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RdRpCATCH> How to use <\/a>\n<!-- Time to render notes section of link id 25763: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25763: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/urgi.versailles.inra.fr\/Tools\/REPET\" id=\"link-23717\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REPET<\/a>\n<!-- Time to render name section of link id 23717: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The<b>\u00a0REPET <\/b><b>package<\/b> (t Flutre <i>et al<\/i>, 2011 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale.<\/p>\n<!-- Time to render link large description section of link id 23717: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REPET> How to use <\/a>\n<!-- Time to render notes section of link id 23717: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23717: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/resfinder\" id=\"link-26087\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ResFinder<\/a>\n<!-- Time to render name section of link id 26087: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.<\/p>\n<!-- Time to render link large description section of link id 26087: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ResFinder> How to use <\/a>\n<!-- Time to render notes section of link id 26087: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26087: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/SwiftSeal\/resistify\" id=\"link-26152\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Resistify<\/a>\n<!-- Time to render name section of link id 26152: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Resistify is a program which rapidly identifies and classifies plant resistance genes from protein sequences. It is designed to be lightweight and easy to use.<\/p>\n<!-- Time to render link large description section of link id 26152: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Resistify> How to use <\/a>\n<!-- Time to render notes section of link id 26152: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26152: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/aldertzomer\/RFPlasmid\" id=\"link-25063\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RFPlasmid<\/a>\n<!-- Time to render name section of link id 25063: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RFPlasmid predicts plasmid contigs from assemblies using single copy marker genes, plasmid genes, and kmers.<\/p>\n<!-- Time to render link large description section of link id 25063: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RFPlasmid> How to use <\/a>\n<!-- Time to render notes section of link id 25063: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25063: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/yaanlpc\/rgaugury\" id=\"link-24496\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RGAugury<\/a>\n<!-- Time to render name section of link id 24496: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A pipeline consisted of a couple of scripts for genome-wide RGAs prediction, most of single script in this package can work independently or together.<\/p>\n<!-- Time to render link large description section of link id 24496: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RGAugury> How to use <\/a>\n<!-- Time to render notes section of link id 24496: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24496: 0.00020694732666016 --> \n<tr><td><a href=\"https:\/\/github.com\/arpcard\/rgi\" id=\"link-24497\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RGI<\/a>\n<!-- Time to render name section of link id 24497: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.<\/p>\n<!-- Time to render link large description section of link id 24497: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RGI> How to use <\/a>\n<!-- Time to render notes section of link id 24497: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24497: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/rvaser\/sift4g\" id=\"link-24723\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SIFT4G<\/a>\n<!-- Time to render name section of link id 24723: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Sorting Intolerant From Tolerant For Genomes.<\/p>\n<!-- Time to render link large description section of link id 24723: 2.6941299438477E-5 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SIFT4G> How to use <\/a>\n<!-- Time to render notes section of link id 24723: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24723: 0.0001368522644043 --> \n<tr><td><a href=\"https:\/\/github.com\/pauline-ng\/SIFT4G_Annotator\" id=\"link-24724\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SIFT4G_Annotator<\/a>\n<!-- Time to render name section of link id 24724: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Annotating VCF files using the SIFT4G databases.<\/p>\n<!-- Time to render link large description section of link id 24724: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24724: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24724: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/KorfLab\/SNAP\" id=\"link-23824\" class=\"track_this_link \" rel=\"noopener noreferrer\">SNAP<\/a>\n<!-- Time to render name section of link id 23824: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Gene prediction tool<\/p>\n<!-- Time to render link large description section of link id 23824: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNAP> How to use <\/a>\n<!-- Time to render notes section of link id 23824: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23824: 0.00011110305786133 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/snoGPS\/\" id=\"link-25293\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snoGPS<\/a>\n<!-- Time to render name section of link id 25293: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Search for H\/ACA snoRNA genes in a genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 25293: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_snoGPS> How to use <\/a>\n<!-- Time to render notes section of link id 25293: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25293: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/snoscan\" id=\"link-25262\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Snoscan<\/a>\n<!-- Time to render name section of link id 25262: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Search for C\/D box methylation guide snoRNA genes in a genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 25262: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Snoscan> How to use <\/a>\n<!-- Time to render notes section of link id 25262: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25262: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/The-Sequence-Ontology\/SOBA\" id=\"link-24528\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SOBAcl<\/a>\n<!-- Time to render name section of link id 24528: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The Sequence Ontology Bioinformatics Analysis command line tool (SOBAcl) will generate a variety of tables, graphs and reports from the data in GFF3 files and format the output in a variety of ways.<\/p>\n<!-- Time to render link large description section of link id 24528: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24528: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24528: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/marcpaga\/sturgeon\" id=\"link-25424\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sturgeon<\/a>\n<!-- Time to render name section of link id 25424: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Sturgeon is a CNS neural network classifier for tumour classification<\/p>\n<!-- Time to render link large description section of link id 25424: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sturgeon> How to use <\/a>\n<!-- Time to render notes section of link id 25424: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25424: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/GonzalezLab\/T-lex3\" id=\"link-24555\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T-lex<\/a>\n<!-- Time to render name section of link id 24555: 2.8610229492188E-6 --> \n<\/td>\n<td><p>T-lex is a computational pipeline that detects presence and\/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data.<\/p>\n<!-- Time to render link large description section of link id 24555: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24555: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24555: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/GenomeRIK\/tama\" id=\"link-24557\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TAMA<\/a>\n<!-- Time to render name section of link id 24557: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Transcriptome Annotation by Modular Algorithms: this software was designed for processing Iso-Seq data and other long read transcriptome data.<\/p>\n<!-- Time to render link large description section of link id 24557: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TAMA> How to use <\/a>\n<!-- Time to render notes section of link id 24557: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24557: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/services.healthtech.dtu.dk\/service.php?TargetP-2.0\" id=\"link-24558\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TargetP<\/a>\n<!-- Time to render name section of link id 24558: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TargetP-2.0 server predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (lTP). For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.<\/p>\n<!-- Time to render link large description section of link id 24558: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TargetP> How to use <\/a>\n<!-- Time to render notes section of link id 24558: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24558: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/cmdcolin\/TEnest\" id=\"link-25488\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TEnest<\/a>\n<!-- Time to render name section of link id 25488: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TEnest is a tool for finding and annotating transposable element (TE) insertions.<\/p>\n<!-- Time to render link large description section of link id 25488: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TEnest> How to use <\/a>\n<!-- Time to render notes section of link id 25488: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25488: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/Tiberius\" id=\"link-25518\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tiberius<\/a>\n<!-- Time to render name section of link id 25518: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tiberius is a deep learning-based ab initio gene structure prediction tool that end-to-end integrates convolutional and long short-term memory layers with a differentiable HMM layer.<\/p>\n<!-- Time to render link large description section of link id 25518: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Tiberius> How to use <\/a>\n<!-- Time to render notes section of link id 25518: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25518: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/danillo-alvarenga\/tn3-ta_finder\" id=\"link-25339\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tn3+TA_finder<\/a>\n<!-- Time to render name section of link id 25339: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Tn3 Transposon\/Toxin Finder (Tn3+TA_finder) is a program for the automatic prediction of transposable elements of the Tn3 family associated with type II toxin and antitoxin pairs in bacteria and archaea.<\/p>\n<!-- Time to render link large description section of link id 25339: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Tn3-TA_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25339: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25339: 0.00012683868408203 --> \n<tr><td><a href=\"https:\/\/github.com\/danillo-alvarenga\/tncomp_finder\" id=\"link-25338\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TnComp_finder<\/a>\n<!-- Time to render name section of link id 25338: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Composite Transposon Finder (TnComp_finder) is a program for the prediction of putative composite transposons in bacterial and archaeal genomes based on insertion sequence replicas in a relatively short span.<\/p>\n<!-- Time to render link large description section of link id 25338: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TnComp_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25338: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25338: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/hillerlab\/TOGA\" id=\"link-25357\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TOGA<\/a>\n<!-- Time to render name section of link id 25357: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost.<\/p>\n<!-- Time to render link large description section of link id 25357: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TOGA> How to use <\/a>\n<!-- Time to render notes section of link id 25357: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25357: 0.00011992454528809 --> \n<tr><td><a href=\"http:\/\/transdecoder.github.io\/\" id=\"link-23750\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TransDecoder<\/a>\n<!-- Time to render name section of link id 23750: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.<\/p>\n<!-- Time to render link large description section of link id 23750: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TransDecoder> How to use <\/a>\n<!-- Time to render notes section of link id 23750: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23750: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/sestaton.github.io\/Transposome\/\" id=\"link-24569\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Transposome<\/a>\n<!-- Time to render name section of link id 24569: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Transposome is a command line application to annotate transposable elements from paired-end whole genome shotgun data.<\/p>\n<!-- Time to render link large description section of link id 24569: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24569: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24569: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/DerKevinRiehl\/transposon_annotation_tools\" id=\"link-24570\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">transposon_annotation_tools<\/a>\n<!-- Time to render name section of link id 24570: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of bioconda packages for transposon annotation and transposon feature annotation in nucleotide sequences. transposon_annotation_tools is part of TransposonUltimate. The package includes a series of transposable element discovery tools, such as: MUSTv2, HelitronScanner, SineFinder, MiteTracker, MiteFinderII, SineScan, TirVish, LtrHarvest, RepeatModeler, TransposonPSI, and TransposonProteinNCBICDD1000. You can then use these tools independently.<\/p>\n<!-- Time to render link large description section of link id 24570: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_transposon_annotation_tools> How to use <\/a>\n<!-- Time to render notes section of link id 24570: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24570: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/DerKevinRiehl\/transposon_classifier_rfsb\" id=\"link-25186\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">transposon_classifier_rfsb<\/a>\n<!-- Time to render name section of link id 25186: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Transposon classification tool for nucleotide sequence classification, providing classification, model training and prediction evaluation. <em>RFSB<\/em> is part of <a href=\"https:\/\/github.com\/DerKevinRiehl\/TransposonUltimate\">TransposonUltimate<\/a>.<\/p>\n<!-- Time to render link large description section of link id 25186: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_transposon_classifier_rfsb> How to use <\/a>\n<!-- Time to render notes section of link id 25186: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25186: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/vlothec\/TRASH\" id=\"link-25165\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TRASH<\/a>\n<!-- Time to render name section of link id 25165: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tandem Repeat Annotation and Structural Hierarchy: a package to identify and extract tandem repeats in genome sequences and investigate their higher order structures.<\/p>\n<!-- Time to render link large description section of link id 25165: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TRASH> How to use <\/a>\n<!-- Time to render notes section of link id 25165: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25165: 0.00011110305786133 --> \n<tr><td><a href=\"http:\/\/trinotate.sourceforge.net\/\" id=\"link-23756\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trinotate<\/a>\n<!-- Time to render name section of link id 23756: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.<\/p>\n<!-- Time to render link large description section of link id 23756: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23756: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23756: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/tRNAscan-SE\/\" id=\"link-23757\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">tRNAscan-SE<\/a>\n<!-- Time to render name section of link id 23757: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Search for tRNA genes in genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 23757: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_tRNAscan-SE> How to use <\/a>\n<!-- Time to render notes section of link id 23757: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23757: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/TSEBRA\" id=\"link-24572\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TSEBRA<\/a>\n<!-- Time to render name section of link id 24572: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start\/stop codons. It was developed to combine BRAKER11 and BRAKER22 predicitons to increase their accuracies.<\/p>\n<!-- Time to render link large description section of link id 24572: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TSEBRA> How to use <\/a>\n<!-- Time to render notes section of link id 24572: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24572: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/VARUS\" id=\"link-24576\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VARUS<\/a>\n<!-- Time to render name section of link id 24576: 3.0994415283203E-6 --> \n<\/td>\n<td><p>VARUS automates the selection and download of a limited number of RNA-seq reads from at NCBI's Sequence Read Archive (SRA) targeting a sufficiently high coverage for many genes for the purpose of gene-finder training and genome annotation.<\/p>\n<!-- Time to render link large description section of link id 24576: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24576: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24576: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/mskcc\/vcf2maf\" id=\"link-24577\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcf2maf<\/a>\n<!-- Time to render name section of link id 24577: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms.<\/p>\n<!-- Time to render link large description section of link id 24577: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcf2maf> How to use <\/a>\n<!-- Time to render notes section of link id 24577: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24577: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/BPRC-Bioinfo\/VDJ-insights\" id=\"link-26180\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VDJ-insights<\/a>\n<!-- Time to render name section of link id 26180: 2.8610229492188E-6 --> \n<\/td>\n<td><p>VDJ-Insights is a robust software package for accurate annotation of the V, D, and J gene segments within immunoglobulin (IG) and T-cell receptor (TCR) genomic regions.<\/p>\n<!-- Time to render link large description section of link id 26180: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VDJ-Insights> How to use <\/a>\n<!-- Time to render notes section of link id 26180: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26180: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/EBI-Metagenomics\/emg-viral-pipeline\" id=\"link-25366\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VIRify<\/a>\n<!-- Time to render name section of link id 25366: 1.9073486328125E-6 --> \n<\/td>\n<td><p>VIRify is a pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies.<\/p>\n<!-- Time to render link large description section of link id 25366: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VIRify> How to use <\/a>\n<!-- Time to render notes section of link id 25366: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25366: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/virulencefinder\" id=\"link-24585\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VirulenceFinder<\/a>\n<!-- Time to render name section of link id 24585: 2.1457672119141E-6 --> \n<\/td>\n<td><p>VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available.<\/p>\n<!-- Time to render link large description section of link id 24585: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24585: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24585: 0.00012707710266113 --> \n<tr><td><a href=\"https:\/\/github.com\/fmaguire\/WoLFPSort\" id=\"link-25469\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WoLFPSort<\/a>\n<!-- Time to render name section of link id 25469: 1.9073486328125E-6 --> \n<\/td>\n<td><p>WoLF PSORT is an extension of the PSORT II program for protein subcellular localization prediction, which is based on the PSORT principle. WoLF PSORT converts a protein's amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs.<\/p>\n<!-- Time to render link large description section of link id 25469: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WoLFPSort> How to use <\/a>\n<!-- Time to render notes section of link id 25469: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25469: 0.00011301040649414 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1124\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => 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Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0039498805999756-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1124 level0\"><!-- Div Category --><div id=\"assembly\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Assembly<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/theaidenlab\/3d-dna\" id=\"link-24131\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">3D-DNA<\/a>\n<!-- Time to render name section of link id 24131: 2.8610229492188E-6 --> \n<\/td>\n<td><p>3D de novo assembly (3D-DNA) pipeline.<\/p>\n<!-- Time to render link large description section of link id 24131: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_3D-DNA> How to use <\/a>\n<!-- Time to render notes section of link id 24131: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24131: 0.00013399124145508 --> \n<tr><td><a href=\"http:\/\/www.bcgsc.ca\/platform\/bioinfo\/software\/abyss\" id=\"link-23578\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ABySS<\/a>\n<!-- Time to render name section of link id 23578: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads.<\/p>\n<!-- Time to render link large description section of link id 23578: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ABySS> How to use <\/a>\n<!-- Time to render notes section of link id 23578: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23578: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/refresh-bio\/agc\" id=\"link-26219\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AGC<\/a>\n<!-- Time to render name section of link id 26219: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. 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The significant difference between ALLPATHS and traditional assemblers such as Arachne is that ALLPATHS assemblies are not necessarily linear, but instead are presented in the form of a graph. This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 23583: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23583: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23583: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/amos\/\" id=\"link-23584\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AMOS<\/a>\n<!-- Time to render name section of link id 23584: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A Modular, Open-Source whole genome assembler.<\/p>\n<!-- Time to render link large description section of link id 23584: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23584: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23584: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/baoxingsong\/anchorwave\" id=\"link-24859\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AnchorWave<\/a>\n<!-- Time to render name section of link id 24859: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals.<\/p>\n<!-- Time to render link large description section of link id 24859: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24859: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24859: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/maiziex\/Aquila\" id=\"link-24139\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Aquila<\/a>\n<!-- Time to render name section of link id 24139: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Diploid personal genome assembly and comprehensive variant detection based on linked-reads.<\/p>\n<!-- Time to render link large description section of link id 24139: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24139: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24139: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/markhilt\/ARBitR\" id=\"link-24140\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARBitR<\/a>\n<!-- Time to render name section of link id 24140: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ARBitR is an overlap aware genome assembly scaffolder for linked sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24140: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24140: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24140: 0.00011014938354492 --> \n<tr><td><a href=\"http:\/\/ibest.github.io\/ARC\/\" id=\"link-24141\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARC<\/a>\n<!-- Time to render name section of link id 24141: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: - Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together. - Reducing\/removing reference bias as compared to mapping based approaches.<\/p>\n<!-- Time to render link large description section of link id 24141: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24141: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24141: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/arcs\/tree\/binomialx2\" id=\"link-23827\" class=\"track_this_link \" rel=\"noopener noreferrer\">ARCS<\/a>\n<!-- Time to render name section of link id 23827: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scaffolding genome sequence assemblies using 10X Genomics GemCode\/Chromium data<\/p>\n<!-- Time to render link large description section of link id 23827: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23827: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23827: 0.00013113021850586 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/arks\" id=\"link-24005\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARKS<\/a>\n<!-- Time to render name section of link id 24005: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scaffolding genome sequence assemblies using 10X Genomics GemCode\/Chromium data. This project is a new kmer-based (alignment free) implementation of ARCS. It provides improved runtime performance over the original ARCS implementation by removing the requirement to perform alignments with bwa mem.<\/p>\n<!-- Time to render link large description section of link id 24005: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24005: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24005: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/iTaxoTools\/ASAPy\" id=\"link-26155\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASAPy<\/a>\n<!-- Time to render name section of link id 26155: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Assemble species by automatic partitioning.<br \/>\r\nThis is a Python wrapper for ASAP.<\/p>\n<!-- Time to render link large description section of link id 26155: 0 --> \n<\/td>\n<td>\n<!-- Time to render notes section of link id 26155: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26155: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/delehef\/asgart\" id=\"link-24105\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASGART<\/a>\n<!-- Time to render name section of link id 24105: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ASGART (A Segmental duplications Gathering and Refinement Tool) is a multiplatform (GNU\/Linux, macOS, Windows) tool designed to search for large duplications amongst one or two DNA strands.<\/p>\n<!-- Time to render link large description section of link id 24105: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24105: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24105: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/ucdavis-bioinformatics\/assemblathon2-analysis\" id=\"link-25078\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">assemblathon2<\/a>\n<!-- Time to render name section of link id 25078: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This repo contains a motley assortment of unpublished scripts and commands used by Ian Korf, Keith Bradnam, and Joe Fass in the analysis of Assemblathon 2 competition entries (assemblies).<\/p>\n<!-- Time to render link large description section of link id 25078: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_assemblathon2> How to use <\/a>\n<!-- Time to render notes section of link id 25078: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25078: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-pathogens\/assembly-stats\" id=\"link-23972\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">assembly-stats<\/a>\n<!-- Time to render name section of link id 23972: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Get assembly statistics from FASTA and FASTQ files.<\/p>\n<!-- Time to render link large description section of link id 23972: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23972: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23972: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/marianattestad\/assemblytics\" id=\"link-24999\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Assemblytics<\/a>\n<!-- Time to render name section of link id 24999: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24999: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24999: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24999: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/yhadevol\/Assexon\" id=\"link-24146\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Assexon<\/a>\n<!-- Time to render name section of link id 24146: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Assembling Exon Using Gene Capture Data<\/p>\n<!-- Time to render link large description section of link id 24146: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24146: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24146: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/juliema\/aTRAM\" id=\"link-24150\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">aTRAM<\/a>\n<!-- Time to render name section of link id 24150: 1.9073486328125E-6 --> \n<\/td>\n<td><p>aTRAM (\"automated target restricted assembly method\") is an iterative assembler that performs reference-guided local de novo assemblies using a variety of available methods.<\/p>\n<!-- Time to render link large description section of link id 24150: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24150: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24150: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Autocycler\" id=\"link-26119\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Autocycler<\/a>\n<!-- Time to render name section of link id 26119: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for generating consensus long-read assemblies for bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 26119: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Autocycler> How to use <\/a>\n<!-- Time to render notes section of link id 26119: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26119: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/Jwindler\/AutoHiC\" id=\"link-25028\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AutoHiC<\/a>\n<!-- Time to render name section of link id 25028: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AutoHiC is a deep learning tool that uses Hi-C data to support genome assembly. It can automatically correct errors during genome assembly and generate genomes at the chromosome level.<\/p>\n<!-- Time to render link large description section of link id 25028: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AutoHiC> How to use <\/a>\n<!-- Time to render notes section of link id 25028: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25028: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/asl\/BandageNG\" id=\"link-25521\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bandage-NG<\/a>\n<!-- Time to render name section of link id 25521: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Bandage-NG is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as SPAdes, MEGAHIT and others.<\/p>\n<!-- Time to render link large description section of link id 25521: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bandage-NG> How to use <\/a>\n<!-- Time to render notes section of link id 25521: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25521: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/github.com\/GATB\/bcalm\" id=\"link-24156\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BCALM2<\/a>\n<!-- Time to render name section of link id 24156: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24156: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24156: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24156: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/pmelsted\/bifrost\" id=\"link-24997\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bifrost<\/a>\n<!-- Time to render name section of link id 24997: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Highly parallel construction and indexing of colored and compacted de Bruijn graphs.<\/p>\n<!-- Time to render link large description section of link id 24997: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bifrost> How to use <\/a>\n<!-- Time to render notes section of link id 24997: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24997: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/institut-de-genomique\/biscot\" id=\"link-24692\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BiSCoT<\/a>\n<!-- Time to render name section of link id 24692: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BiSCoT is a tool that aims to improve the contiguity of scaffolds and contigs generated after a Bionano scaffolding.<\/p>\n<!-- Time to render link large description section of link id 24692: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24692: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24692: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/github.com\/fmaguire\/Bridger_Assembler\" id=\"link-24746\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bridger<\/a>\n<!-- Time to render name section of link id 24746: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bridger is an efficient de novo trascriptome assembler for RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 24746: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bridger> How to use <\/a>\n<!-- Time to render notes section of link id 24746: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24746: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/busco.ezlab.org\/v2\/\" id=\"link-23844\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BUSCO<\/a>\n<!-- Time to render name section of link id 23844: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BUSCO v2 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9. BUSCO assessments are implemented in open-source software, with a large selection of lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.<\/p>\n<!-- Time to render link large description section of link id 23844: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BUSCO> How to use <\/a>\n<!-- Time to render notes section of link id 23844: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23844: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/jamiemcg\/BUSCO_phylogenomics\" id=\"link-25092\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BUSCO_phylogenomics<\/a>\n<!-- Time to render name section of link id 25092: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is a Python pipeline to construct species phylogenies using BUSCO proteins. It works directly from BUSCO output and can generate concatenated supermatrix alignments and also gene trees of BUSCO families.<\/p>\r\n<p dir=\"auto\">The pipeline identifies BUSCO proteins that are complete and single-copy in all input samples. Alternatively, you can account for missing data and choose to include BUSCO proteins that are complete and single-copy in a certain percentage of input samples. Each BUSCO family is individually aligned, trimmed, and then concatenated together to generate a supermatrix alignment. The pipeline also identifies BUSCO proteins that are complete and single-copy in at least 4 input samples, and generates gene trees for each of these families.<\/p>\n<!-- Time to render link large description section of link id 25092: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BUSCO_phylogenomics> How to use <\/a>\n<!-- Time to render notes section of link id 25092: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25092: 0.00010204315185547 --> \n<tr><td><a href=\"https:\/\/github.com\/Malfoy\/BWISE\" id=\"link-24170\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BWISE<\/a>\n<!-- Time to render name section of link id 24170: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software for genome assembly using short-reads.<\/p>\n<!-- Time to render link large description section of link id 24170: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BWISE> How to use <\/a>\n<!-- Time to render notes section of link id 24170: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24170: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/CAMI-challenge\/AMBER\" id=\"link-24671\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAMI-AMBER<\/a>\n<!-- Time to render name section of link id 24671: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets.<\/p>\n<!-- Time to render link large description section of link id 24671: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24671: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24671: 0.00012493133544922 --> \n<tr><td><a href=\"https:\/\/github.com\/EBI-Metagenomics\/emg-viral-pipeline\" id=\"link-25569\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAMISIM<\/a>\n<!-- Time to render name section of link id 25569: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CAMISIM is a software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets.<\/p>\n<!-- Time to render link large description section of link id 25569: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAMISIM> How to use <\/a\n<!-- Time to render notes section of link id 25569: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25569: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/canu\" id=\"link-23781\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">canu<\/a>\n<!-- Time to render name section of link id 23781: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A single molecule sequence assembler for genomes large and small.<\/p>\n<!-- Time to render link large description section of link id 23781: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Canu> How to use <\/a>\n<!-- Time to render notes section of link id 23781: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23781: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/seq.cs.iastate.edu\/\" id=\"link-24054\" class=\"track_this_link \" rel=\"noopener noreferrer\">CAP3<\/a>\n<!-- Time to render name section of link id 24054: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A DNA Sequence Assembly Program<\/p>\n<!-- Time to render link large description section of link id 24054: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAP3> How to use <\/a>\n<!-- Time to render notes section of link id 24054: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24054: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/kamimrcht\/CARNAC-LR\" id=\"link-24000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CARNAC-LR<\/a>\n<!-- Time to render name section of link id 24000: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Clustering coefficient-based Acquisition of RNA Communities in Long Reads.<\/p>\n<!-- Time to render link large description section of link id 24000: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24000: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24000: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/ecogenomics.github.io\/CheckM\/\" id=\"link-25097\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CheckM<\/a>\n<!-- Time to render name section of link id 25097: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.<\/p>\n<!-- Time to render link large description section of link id 25097: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CheckM> How to use <\/a>\n<!-- Time to render notes section of link id 25097: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25097: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/estebanpw\/chromeister\" id=\"link-24177\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chromeister<\/a>\n<!-- Time to render name section of link id 24177: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A dotplot generator for large chromosomes.<\/p>\n<!-- Time to render link large description section of link id 24177: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chromeister> How to use <\/a>\n<!-- Time to render notes section of link id 24177: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24177: 0.00011610984802246 --> \n<tr><td><a href=\"http:\/\/catchenlab.life.illinois.edu\/chromonomer\/\" id=\"link-24178\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Chromonomer<\/a>\n<!-- Time to render name section of link id 24178: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Chromonomer is a program designed to integrate a genome assembly with a genetic map.<\/p>\n<!-- Time to render link large description section of link id 24178: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24178: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24178: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/sanger-pathogens.github.io\/circlator\/\" id=\"link-23802\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Circlator<\/a>\n<!-- Time to render name section of link id 23802: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool to circularize genome assemblies<\/p>\n<!-- Time to render link large description section of link id 23802: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Circlator> How to use <\/a>\n<!-- Time to render notes section of link id 23802: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23802: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/vtsyvina\/CliqueSNV\" id=\"link-24867\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CliqueSNV<\/a>\n<!-- Time to render name section of link id 24867: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scalable Reconstruction of Intra-Host Viral Populations from NGS Reads.<\/p>\n<!-- Time to render link large description section of link id 24867: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24867: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24867: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/ziyewang\/COMEBin\" id=\"link-25576\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">COMEBin<\/a>\n<!-- Time to render name section of link id 25576: 2.8610229492188E-6 --> \n<\/td>\n<td><p>COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning.<\/p>\n<!-- Time to render link large description section of link id 25576: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_COMEBin> How to use <\/a>\n<!-- Time to render notes section of link id 25576: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25576: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/huangnengCSU\/compleasm\" id=\"link-25251\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">compleasm<\/a>\n<!-- Time to render name section of link id 25251: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A genome completeness evaluation tool based on miniprot.<\/p>\n<!-- Time to render link large description section of link id 25251: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_compleasm> How to use <\/a>\n<!-- Time to render notes section of link id 25251: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25251: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/culebront-pipeline.readthedocs.io\/en\/latest\/\" id=\"link-24189\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CulebrONT<\/a>\n<!-- Time to render name section of link id 24189: 2.8610229492188E-6 --> \n<\/td>\n<td><p>An open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple assembly tools in parallel, giving you the possibility of circularise, polish, and correct assemblies, checking quality. CulebrONT can help to choose the best assembly between all possibilities.<\/p>\n<!-- Time to render link large description section of link id 24189: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24189: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24189: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/MartinPippel\/DAmar\" id=\"link-24191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAmar<\/a>\n<!-- Time to render name section of link id 24191: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Long read QC, assembly and scaffolding pipeline for PacBio or Oxford Nanopore long-read sequencing data. T he pipeline produces a number of QC metrics at various stages as well as incorporating further technologies including Bionano, 10x and HiC data to scaffold the created contigs. DAmar, is a hybrid of the earlier Marvel, Dazzler, and Daccord systems of the Eugene Myers lab.<\/p>\n<!-- Time to render link large description section of link id 24191: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24191: 7.8678131103516E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24191: 0.00012302398681641 --> \n<tr><td><a href=\"https:\/\/github.com\/thegenemyers\/DAZZ_DB\" id=\"link-23614\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAZZ_DB<\/a>\n<!-- Time to render name section of link id 23614: 3.0994415283203E-6 --> \n<\/td>\n<td><p>To facilitate the multiple phases of the dazzler assembler, we organize all the read data into what is effectively a \"database\" of the reads and their meta-information.<\/p>\n<!-- Time to render link large description section of link id 23614: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23614: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23614: 0.0001218318939209 --> \n<tr><td><a href=\"https:\/\/github.com\/yechengxi\/DBG2OLC\" id=\"link-24047\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DBG2OLC<\/a>\n<!-- Time to render name section of link id 24047: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24047: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24047: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24047: 0.0001220703125 --> \n<tr><td><a href=\"https:\/\/github.com\/a-ludi\/dentist\" id=\"link-24198\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DENTIST<\/a>\n<!-- Time to render name section of link id 24198: 1.9073486328125E-6 --> \n<\/td>\n<td><p>DENTIST is a sensitive, highly-accurate and automated pipeline method to close gaps in (short read) assemblies with long reads.<\/p>\n<!-- Time to render link large description section of link id 24198: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24198: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24198: 0.00011897087097168 --> \n<tr><td><a href=\"http:\/\/www.broadinstitute.org\/software\/discovar\/blog\/\" id=\"link-24201\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Discovar<\/a>\n<!-- Time to render name section of link id 24201: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Assemble genomes and find variants with DISCOVAR &amp; DISCOVAR\u00a0de\u00a0novo<\/p>\n<!-- Time to render link large description section of link id 24201: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24201: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24201: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/www.sigenae.org\/drap\/index.html\" id=\"link-23788\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">drap<\/a>\n<!-- Time to render name section of link id 23788: 1.9073486328125E-6 --> \n<\/td>\n<td><p>De novo RNA-seq Assembly Pipeline<\/p>\n<!-- Time to render link large description section of link id 23788: 0 --> \n<\/td>\n<td>strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DRAP> How to use <\/a>\n<!-- Time to render notes section of link id 23788: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23788: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/MrOlm\/drep\" id=\"link-24203\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dRep<\/a>\n<!-- Time to render name section of link id 24203: 1.9073486328125E-6 --> \n<\/td>\n<td><p>dRep is a python program for rapidly comparing large numbers of genomes. dRep can also \"de-replicate\" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.<\/p>\n<!-- Time to render link large description section of link id 24203: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dRep> How to use <\/a>\n<!-- Time to render notes section of link id 24203: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24203: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/cgm.sjtu.edu.cn\/eupan\/\" id=\"link-24220\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EUPAN<\/a>\n<!-- Time to render name section of link id 24220: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Toolkit that integrates various software in order to build eukaryotic pangenomes.<\/p>\n<!-- Time to render link large description section of link id 24220: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24220: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24220: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/FABuLOUS\" id=\"link-24222\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FABuLOUS<\/a>\n<!-- Time to render name section of link id 24222: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly. Initially called TGS-GapCloser.<\/p>\n<!-- Time to render link large description section of link id 24222: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24222: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24222: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/falcon\" id=\"link-23622\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON<\/a>\n<!-- Time to render name section of link id 23622: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Falcon: a set of tools for fast aligning long reads for consensus and assembly<\/p>\n<!-- Time to render link large description section of link id 23622: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23622: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23622: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/FALCON_unzip\" id=\"link-24282\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON_unzip<\/a>\n<!-- Time to render name section of link id 24282: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Making diploid assembly becomes common practice for genomic study<\/p>\n<!-- Time to render link large description section of link id 24282: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24282: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24282: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/phasegenomics\/FALCON-Phase\" id=\"link-24038\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON-Phase<\/a>\n<!-- Time to render name section of link id 24038: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds.<\/p>\n<!-- Time to render link large description section of link id 24038: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24038: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24038: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/mrmckain\/Fast-Plast\" id=\"link-24227\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Fast-Plast<\/a>\n<!-- Time to render name section of link id 24227: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and verify whole chloroplast genome sequences.<\/p>\n<!-- Time to render link large description section of link id 24227: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24227: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24227: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/fcs\" id=\"link-25990\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FCS<\/a>\n<!-- Time to render name section of link id 25990: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The NCBI Foreign Contamination Screen (FCS) is a tool suite (FCS-adaptator et FCS-gx) for identifying and removing contaminant sequences in genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 25990: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FCS> How to use <\/a>\n<!-- Time to render notes section of link id 25990: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25990: 0.00011897087097168 --> \n<tr><td><a href=\"http:\/\/www.cbcb.umd.edu\/software\/flash\" id=\"link-23629\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLASH<\/a>\n<!-- Time to render name section of link id 23629: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 23629: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FLASH> How to use <\/a>\n<!-- Time to render notes section of link id 23629: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23629: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/fenderglass\/Flye\" id=\"link-24015\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Flye<\/a>\n<!-- Time to render name section of link id 24015: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.<\/p>\n<!-- Time to render link large description section of link id 24015: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Flye> How to use <\/a>\n<!-- Time to render notes section of link id 24015: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24015: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/jwanglab\/fmlrc2\" id=\"link-25112\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FMLRC2<\/a>\n<!-- Time to render name section of link id 25112: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FMLRC2 performs error correction\/polishing of long erroneous sequences with accurate short reads. As such, it can be used as\u00a0<em>both<\/em>\u00a0an error-correction tool <<a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2051-3\" rel=\"nofollow\">1<\/a>> for raw long reads (ex. Oxford Nanopore)\u00a0<em>and<\/em>\u00a0a polishing tool <<a href=\"http:\/\/biorxiv.org\/content\/early\/2022\/07\/23\/2022.07.22.501182\" rel=\"nofollow\">2<\/a>> for\u00a0<em>de novo<\/em>\u00a0assemblies.<\/p>\n<!-- Time to render link large description section of link id 25112: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FMLRC2> How to use <\/a>\n<!-- Time to render notes section of link id 25112: 7.8678131103516E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25112: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/github.com\/NBISweden\/GAAS\" id=\"link-24242\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GAAS<\/a>\n<!-- Time to render name section of link id 24242: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Genome Assembly Annotation Service: Suite of tools related to Genome Assembly Annotation Service tasks.<\/p>\n<!-- Time to render link large description section of link id 24242: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24242: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24242: 0.00012016296386719 --> \n<tr><td><a href=\"http:\/\/soap.genomics.org.cn\/about.html#resource2\" id=\"link-23633\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GapCloser<\/a>\n<!-- Time to render name section of link id 23633: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo, using the abundant pair relationships of short reads.<\/p>\n<!-- Time to render link large description section of link id 23633: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GapCloser> How to use <\/a>\n<!-- Time to render notes section of link id 23633: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23633: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/yeeus\/GCI.git\" id=\"link-25561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GCI<\/a>\n<!-- Time to render name section of link id 25561: 1.9073486328125E-6 --> \n<\/td>\n<td>Genome Continuity Inspector (GCI) is an assembly assessment tool for high-quality genomes (e.g. T2T genomes), in base resolution.\n<!-- Time to render link large description section of link id 25561: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCI> How to use <\/a>\n<!-- Time to render notes section of link id 25561: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25561: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/tbenavi1\/genomescope2.0\" id=\"link-24248\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeScope2.0<\/a>\n<!-- Time to render name section of link id 24248: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Reference-free profiling of polyploid genomes<\/p>\n<!-- Time to render link large description section of link id 24248: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeScope2.0> How to use <\/a>\n<!-- Time to render notes section of link id 24248: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24248: 0.00010085105895996 --> \n<tr><td><a href=\"https:\/\/github.com\/Kinggerm\/GetOrganelle\" id=\"link-24251\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GetOrganelle<\/a>\n<!-- Time to render name section of link id 24251: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This toolkit assemblies organelle genome from genomic skimming data.<\/p>\n<!-- Time to render link large description section of link id 24251: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GetOrganelle> How to use <\/a>\n<!-- Time to render notes section of link id 24251: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24251: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/vgl-hub\/gfastats\" id=\"link-24253\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gfastats<\/a>\n<!-- Time to render name section of link id 24253: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa <.gz>) genome assembly file manipulation.<\/p>\n<!-- Time to render link large description section of link id 24253: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24253: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24253: 0.00027704238891602 --> \n<tr><td><a href=\"https:\/\/odelaneau.github.io\/GLIMPSE\/index.html\" id=\"link-24258\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GLIMPSE<\/a>\n<!-- Time to render name section of link id 24258: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.<\/p>\n<!-- Time to render link large description section of link id 24258: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GLIMPSE> How to use <\/a>\n<!-- Time to render notes section of link id 24258: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24258: 0.00012516975402832 --> \n<tr><td><a href=\"https:\/\/github.com\/nadegeguiglielmoni\/GraphUnzip\" id=\"link-24702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphUnzip<\/a>\n<!-- Time to render name section of link id 24702: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Unzip assembly graphs with Hi-C data and\/or long reads.<\/p>\n<!-- Time to render link large description section of link id 24702: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24702: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24702: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/rolandfaure\/hairsplitter\" id=\"link-26093\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hairsplitter<\/a>\n<!-- Time to render name section of link id 26093: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.<\/p>\n<!-- Time to render link large description section of link id 26093: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hairsplitter> How to use <\/a>\n<!-- Time to render notes section of link id 26093: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26093: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/smajidian\/Hap10\" id=\"link-24270\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hap10<\/a>\n<!-- Time to render name section of link id 24270: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The goal is to reconstruct accurate and long haplotypes polyploid genome using linked reads.<\/p>\n<!-- Time to render link large description section of link id 24270: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24270: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24270: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/zengxiaofei\/HapHiC\" id=\"link-26013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HapHiC<\/a>\n<!-- Time to render name section of link id 26013: 3.0994415283203E-6 --> \n<\/td>\n<td><p>HapHiC is an allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules.<\/p>\n<!-- Time to render link large description section of link id 26013: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HapHiC> How to use <\/a>\n<!-- Time to render notes section of link id 26013: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26013: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/gwcbi\/haphpipe\" id=\"link-25171\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HAPHPIPE<\/a>\n<!-- Time to render name section of link id 25171: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NGS viral assembly and population genetics.<\/p>\n<!-- Time to render link large description section of link id 25171: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HAPHPIPE> How to use <\/a>\n<!-- Time to render notes section of link id 25171: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25171: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/Nobel-Justin\/HaploHiC\" id=\"link-24272\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HaploHiC<\/a>\n<!-- Time to render name section of link id 24272: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Comprehensive haplotype division of Hi-C PE-reads based on local contacts ratio.<\/p>\n<!-- Time to render link large description section of link id 24272: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24272: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24272: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/mapleforest\/HaploMerger2\" id=\"link-23846\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HaploMerger2<\/a>\n<!-- Time to render name section of link id 23846: 1.9073486328125E-6 --> \n<\/td>\n<td><p>&lt;HaploMerger2 (HM2) is an important upgrade over HaploMerger. HM2 is an easy-to-use automated pipeline for improving genome assembly in the post-assembly stage. It consists of a set of executables as well as wrappers for several third-part software.<\/p>\n<!-- Time to render link large description section of link id 23846: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23846: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23846: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/institut-de-genomique\/HAPO-G\" id=\"link-24274\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hapo-G<\/a>\n<!-- Time to render name section of link id 24274: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.<\/p>\n<!-- Time to render link large description section of link id 24274: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hapo-G> How to use <\/a>\n<!-- Time to render notes section of link id 24274: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24274: 0.00012612342834473 --> \n<tr><td><a href=\"https:\/\/github.com\/vpc-ccg\/haslr\" id=\"link-24275\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HASLR<\/a>\n<!-- Time to render name section of link id 24275: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.<\/p>\n<!-- Time to render link large description section of link id 24275: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24275: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24275: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/maxplanck-ie\/HiCAssembler\" id=\"link-25725\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HiCAssembler<\/a>\n<!-- Time to render name section of link id 25725: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software to assemble contigs\/scaffolds into chromosomes using Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 25725: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiCAssembler> How to use <\/a>\n<!-- Time to render notes section of link id 25725: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25725: 0.00012302398681641 --> \n<tr><td><a href=\"https:\/\/github.com\/chhylp123\/hifiasm\" id=\"link-24292\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\">hifiasm<\/a>\n<!-- Time to render name section of link id 24292: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome.<\/p>\n<!-- Time to render link large description section of link id 24292: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hifiasm> How to use <\/a>\n<!-- Time to render notes section of link id 24292: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24292: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/xfengnefx\/hifiasm-meta\" id=\"link-24293\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\">hifiasm-meta<\/a>\n<!-- Time to render name section of link id 24293: 2.1457672119141E-6 --> \n<\/td>\n<td><p>De novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.<\/p>\n<!-- Time to render link large description section of link id 24293: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hifiasm-meta> How to use <\/a>\n<!-- Time to render notes section of link id 24293: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24293: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0020\" id=\"link-24747\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IBA<\/a>\n<!-- Time to render name section of link id 24747: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python script to assemble AHE (Anchored Hybrid Enrichment) data loci by loci. To summarize, raw sequencing reads for each species were filtered for quality using Trim Galore! v. 0.4.0 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b9005\" name=\"bb9005\"><span class=\"anchor-text\">Krueger, 2015<\/span><\/a>), and assembled using the iterative baited assembly (IBA) Python script which employs USEARCH v. 7.0 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0060\" name=\"bb0060\"><span class=\"anchor-text\">Edgar, 2010<\/span><\/a>) and Bridger v. 2014-12-01 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0030\" name=\"bb0030\"><span class=\"anchor-text\">Chang et al., 2015<\/span><\/a>) to assemble loci for each taxon. MAFFT v. 7.245 (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0160\" name=\"bb0160\"><span class=\"anchor-text\">Katoh and Standley, 2013<\/span><\/a>) was used to align assembled sequences, and the probe and\u00a0<a class=\"topic-link\" title=\"Learn more about flanking regions from ScienceDirect's AI-generated Topic Pages\" href=\"https:\/\/www.sciencedirect.com\/topics\/biochemistry-genetics-and-molecular-biology\/dna-flanking-region\">flanking regions<\/a>\u00a0were separated with the Python script Extract_probe_region.py (<a class=\"anchor workspace-trigger u-display-inline anchor-paragraph\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1055790318302112#b0020\" name=\"bb0020\"><span class=\"anchor-text\">Breinholt et al., 2018<\/span><\/a>).<\/p>\n<!-- Time to render link large description section of link id 24747: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24747: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24747: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/ChongLab\/Inspector\" id=\"link-24299\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Inspector<\/a>\n<!-- Time to render name section of link id 24299: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool for evaluate long-read de novo assembly results.<\/p>\n<!-- Time to render link large description section of link id 24299: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Inspector> How to use <\/a>\n<!-- Time to render notes section of link id 24299: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24299: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbbioconda\/wiki\/Improved-Phased-Assembler\" id=\"link-24323\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IPA<\/a>\n<!-- Time to render name section of link id 24323: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly.<\/p>\n<!-- Time to render link large description section of link id 24323: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IPA> How to use <\/a>\n<!-- Time to render notes section of link id 24323: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24323: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/wonder.cdc.gov\/amd\/flu\/irma\/\" id=\"link-24325\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IRMA<\/a>\n<!-- Time to render name section of link id 24325: 1.9073486328125E-6 --> \n<\/td>\n<td><p>IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza and ebolavirus. IRMA is free to use and parallelizes computations for both cluster computing and single computer multi-core setups.<\/p>\n<!-- Time to render link large description section of link id 24325: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IRMA> How to use <\/a>\n<!-- Time to render notes section of link id 24325: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24325: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/alumni.cs.ucr.edu\/~liw\/isolasso.html\" id=\"link-24327\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IsoLasso<\/a>\n<!-- Time to render name section of link id 24327: 2.1457672119141E-6 --> \n<\/td>\n<td><p>IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.<\/p>\n<!-- Time to render link large description section of link id 24327: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24327: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24327: 0.00011014938354492 --> \n<tr><td><a href=\"http:\/\/sanger-pathogens.github.io\/iva\/\" id=\"link-23945\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IVA<\/a>\n<!-- Time to render name section of link id 23945: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Iterative Virus Assembler is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth<\/p>\n<!-- Time to render link large description section of link id 23945: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23945: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23945: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/alguoo314\/jasper\" id=\"link-25059\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JASPER<\/a>\n<!-- Time to render name section of link id 25059: 1.9073486328125E-6 --> \n<\/td>\n<td><p dir=\"auto\">JASPER (Jellyfish based Assembly Sequence Polisher for Error Reduction) is an efficient polishing tool for draft genomes. It uses accurate reads (PacBio HiFi or Illumina) to evaluate consensus quality and correct consensus errors in genome assemblies. JASPER is substantially faster than polishing methods based on sequence alignment, and more accurate than currently available k-mer based methods. The efficiency and scalability of JASPER allows one to use it to create personalized reference genomes for specific populations very efficiently, even for large sequenced populations, by polishing the reference genome, such as GRCh38 or chm13v2.0 for human, with Illumina reads sequenced from many individuals from the population.<\/p>\r\n<p dir=\"auto\">Please see this manuscript for more details: Guo A, Salzberg SL, Zimin AV. JASPER: A fast genome polishing tool that improves accuracy of genome assemblies. PLoS Comput Biol. 2023 Mar 31;19(3):e1011032. doi: 10.1371\/journal.pcbi.1011032. PMID: 37000853; PMCID: PMC10096238.<\/p>\n<!-- Time to render link large description section of link id 25059: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JASPER> How to use <\/a>\n<!-- Time to render notes section of link id 25059: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25059: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/ban-m\/jtk\" id=\"link-24958\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JTK<\/a>\n<!-- Time to render name section of link id 24958: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A regional diploid genome assembler.<\/p>\n<!-- Time to render link large description section of link id 24958: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JTK> How to use <\/a>\n<!-- Time to render notes section of link id 24958: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24958: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/liu3zhenlab\/kad\" id=\"link-24335\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KAD<\/a>\n<!-- Time to render name section of link id 24335: 3.0994415283203E-6 --> \n<\/td>\n<td><p>KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24335: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24335: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24335: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/dib-lab\/khmer\" id=\"link-26171\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">khmer<\/a>\n<!-- Time to render name section of link id 26171: 2.8610229492188E-6 --> \n<\/td>\n<td><p>In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more.<\/p>\r\n<p><a href=\"https:\/\/khmer.readthedocs.io\/en\/latest\/\">The khmer software for advanced biological sequencing data analysis \u2014 khmer 3.0.0a1+98.gfe0ce11 documentation<\/a><\/p>\n<!-- Time to render link large description section of link id 26171: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_khmer> How to use <\/a>\n<!-- Time to render notes section of link id 26171: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26171: 0.00011181831359863 --> \n<tr><td><a href=\"https:\/\/catchenlab.life.illinois.edu\/klumpy\/\" id=\"link-26205\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">klumpy<\/a>\n<!-- Time to render name section of link id 26205: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Klumpy is a bioinformatic tool for identifying possibly incorrectly assembled regions in a long-read based assembly, with the additional capabilities of annotating sequences given a set of query sequences.<\/p>\n<!-- Time to render link large description section of link id 26205: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_klumpy> How to use <\/a>\n<!-- Time to render notes section of link id 26205: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26205: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/sun.aei.polsl.pl\/REFRESH\/index.php?page=projects&#038;#038\" id=\"link-24339\" class=\"track_this_link \" rel=\"noopener noreferrer\">KMC<\/a>\n<!-- Time to render name section of link id 24339: 1.9073486328125E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 24339: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KMC> How to use <\/a>\n<!-- Time to render notes section of link id 24339: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24339: 0.00011396408081055 --> \n<tr><td><a href=\"http:\/\/kmergenie.bx.psu.edu\/\" id=\"link-23652\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KmerGenie<\/a>\n<!-- Time to render name section of link id 23652: 1.9073486328125E-6 --> \n<\/td>\n<td><p>KmerGenie estimates the best k-mer length for genome de novo assembly.<\/p>\n<!-- Time to render link large description section of link id 23652: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KmerGenie> How to use <\/a>\n<!-- Time to render notes section of link id 23652: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23652: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/shendurelab\/LACHESIS\" id=\"link-23932\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LACHESIS<\/a>\n<!-- Time to render name section of link id 23932: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software that uses Hi-C data for ultra-long-range scaffolding of de novo genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 23932: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23932: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23932: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/mcfrith\/lamassemble\" id=\"link-24341\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lamassemble<\/a>\n<!-- Time to render name section of link id 24341: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Merge overlapping \"long\" DNA reads into a consensus sequence.<\/p>\n<!-- Time to render link large description section of link id 24341: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24341: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24341: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/rwtourdot\/linker\" id=\"link-24348\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Linker<\/a>\n<!-- Time to render name section of link id 24348: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Linker is a suite of C++ tools useful for interpreting long and linked read sequencing of cancer genomes.<\/p>\n<!-- Time to render link large description section of link id 24348: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24348: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24348: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/LINKS\" id=\"link-23936\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LINKS<\/a>\n<!-- Time to render name section of link id 23936: 1.9073486328125E-6 --> \n<\/td>\n<td><p>LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences.<\/p>\n<!-- Time to render link large description section of link id 23936: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LINKS> How to use <\/a>\n<!-- Time to render notes section of link id 23936: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23936: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/AntonBankevich\/LJA\" id=\"link-24350\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LJA<\/a>\n<!-- Time to render name section of link id 24350: 2.1457672119141E-6 --> \n<\/td>\n<td><p>La Jolla Assembler (LJA) is a tool for genome assembly from HiFI reads based on de Bruijn graphs.<\/p>\n<!-- Time to render link large description section of link id 24350: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LJA> How to use <\/a>\n<!-- Time to render notes section of link id 24350: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24350: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/longstitch\" id=\"link-24356\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LongStitch<\/a>\n<!-- Time to render name section of link id 24356: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A genome assembly correction and scaffolding pipeline using long reads. Basically runs Tigmint, ntLink, ARKS.<\/p>\n<!-- Time to render link large description section of link id 24356: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24356: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24356: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/www.fishbrowser.org\/software\/LR_Gapcloser\/index.php\/Home\/Index\/Index.html\" id=\"link-24030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LR_Gapcloser<\/a>\n<!-- Time to render name section of link id 24030: 2.1457672119141E-6 --> \n<\/td>\n<td><p>\u00a0LR_Gapcloser is a gap closing tool using uncorrected or corrected long reads generated from Pacbio platform or Nanopore platform.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24030: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24030: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24030: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/shingocat\/lrscaf\" id=\"link-23977\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRScaf<\/a>\n<!-- Time to render name section of link id 23977: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TGS scaffolding . Improving draft genomes using long noisy reads.<\/p>\n<!-- Time to render link large description section of link id 23977: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23977: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23977: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/aquaskyline\/LRSIM\" id=\"link-24358\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRSIM<\/a>\n<!-- Time to render name section of link id 24358: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Simulator for Linked Reads: this package simulates whole genome sequencing using 10X Genomics Linked Read technology.<\/p>\n<!-- Time to render link large description section of link id 24358: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24358: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24358: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/oushujun\/LTR_retriever\" id=\"link-24856\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LTR_retriever<\/a>\n<!-- Time to render name section of link id 24856: 1.9073486328125E-6 --> \n<\/td>\n<td><p>LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons.<\/p>\n<!-- Time to render link large description section of link id 24856: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LTR_retriever> How to use <\/a>\n<!-- Time to render notes section of link id 24856: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24856: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/colibread.inria.fr\/software\/mapsembler2\/\" id=\"link-23935\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mapsembler2<\/a>\n<!-- Time to render name section of link id 23935: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Mapsembler2 is a targeted assembly software. It takes as input any number of NGS raw read set(s) (fasta or fastq, gzipped or not) and a set of input sequences (starters).<\/p>\n<!-- Time to render link large description section of link id 23935: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23935: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23935: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/schloi\/MARVEL\" id=\"link-23888\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MARVEL<\/a>\n<!-- Time to render name section of link id 23888: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.<\/p>\n<!-- Time to render link large description section of link id 23888: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23888: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23888: 0.00011420249938965 --> \n<tr><td><a href=\"http:\/\/www.genome.umd.edu\/masurca.html\" id=\"link-23661\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MaSuRCA<\/a>\n<!-- Time to render name section of link id 23661: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MaSuRCA is whole genome assembly software. It combines the efficiency of the de\u00a0Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454)<\/p>\n<!-- Time to render link large description section of link id 23661: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MaSuRCA> How to use <\/a>\n<!-- Time to render notes section of link id 23661: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23661: 0.00014710426330566 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/matchap\/\" id=\"link-24368\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAtCHap<\/a>\n<!-- Time to render name section of link id 24368: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An ultra fast algorithm for solving the single individual haplotype assembly problem.<\/p>\n<!-- Time to render link large description section of link id 24368: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24368: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24368: 0.00013113021850586 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/MECAT\" id=\"link-23979\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MECAT<\/a>\n<!-- Time to render name section of link id 23979: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads.<\/p>\n<!-- Time to render link large description section of link id 23979: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23979: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23979: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/voutcn\/megahit\" id=\"link-23780\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEGAHIT<\/a>\n<!-- Time to render name section of link id 23780: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph<\/p>\n<!-- Time to render link large description section of link id 23780: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MEGAHIT> How to use <\/a>\n<!-- Time to render notes section of link id 23780: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23780: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/LANL-Bioinformatics\/MeGAMerge\" id=\"link-23925\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MeGAMerge<\/a>\n<!-- Time to render name section of link id 23925: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool to merge assembled contigs, long reads from metagenomic sequencing runs<\/p>\n<!-- Time to render link large description section of link id 23925: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23925: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23925: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/merqury\" id=\"link-24372\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Merqury<\/a>\n<!-- Time to render name section of link id 24372: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Evaluate genome assemblies with k-mers and more<\/p>\n<!-- Time to render link large description section of link id 24372: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Merqury> How to use <\/a>\n<!-- Time to render notes section of link id 24372: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24372: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/meryl\" id=\"link-24373\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Meryl<\/a>\n<!-- Time to render name section of link id 24373: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A genomic k-mer counter (and sequence utility) with nice features.<\/p>\n<!-- Time to render link large description section of link id 24373: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Meryl> How to use <\/a>\n<!-- Time to render notes section of link id 24373: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24373: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/GaetanBenoitDev\/metaMDBG\" id=\"link-25473\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaMDBG<\/a>\n<!-- Time to render name section of link id 25473: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A lightweight assembler for long and accurate metagenomics reads.<\/p>\n<!-- Time to render link large description section of link id 25473: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaMDBG> How to use <\/a>\n<!-- Time to render notes section of link id 25473: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25473: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/bxlab\/metaWRAP\" id=\"link-24377\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaWRAP<\/a>\n<!-- Time to render name section of link id 24377: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A flexible pipeline for genome-resolved metagenomic data analysis.<\/p>\n<!-- Time to render link large description section of link id 24377: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaWRAP> How to use <\/a>\n<!-- Time to render notes section of link id 24377: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24377: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bpucker\/MGSE\" id=\"link-24120\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MGSE<\/a>\n<!-- Time to render name section of link id 24120: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly.<\/p>\n<!-- Time to render link large description section of link id 24120: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24120: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24120: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/miniasm\" id=\"link-23810\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniasm<\/a>\n<!-- Time to render name section of link id 23810: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Ultrafast de novo assembly for long noisy reads (though having no consensus step).<\/p>\n<!-- Time to render link large description section of link id 23810: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniasm> How to use <\/a>\n<!-- Time to render notes section of link id 23810: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23810: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/huangnengCSU\/minibusco\" id=\"link-24871\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiniBUSCO<\/a>\n<!-- Time to render name section of link id 24871: 7.8678131103516E-6 --> \n<\/td>\n<td><p>A genome completeness evaluation tool based on miniprot.<\/p>\n<!-- Time to render link large description section of link id 24871: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MiniBUSCO> How to use <\/a>\n<!-- Time to render notes section of link id 24871: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24871: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Minipolish\" id=\"link-24384\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minipolish<\/a>\n<!-- Time to render name section of link id 24384: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool for Racon polishing of miniasm assemblies.<\/p>\n<!-- Time to render link large description section of link id 24384: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minipolish> How to use <\/a>\n<!-- Time to render notes section of link id 24384: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24384: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/mira-assembler\" id=\"link-23667\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MIRA<\/a>\n<!-- Time to render name section of link id 23667: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Whole genome shotgun and EST sequence assembler for Sanger, 454, and Solexa \/ Illumina.<\/p>\n<!-- Time to render link large description section of link id 23667: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MIRA> How to use <\/a>\n<!-- Time to render notes section of link id 23667: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23667: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/pedronachtigall\/MITGARD\" id=\"link-24674\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MITGARD<\/a>\n<!-- Time to render name section of link id 24674: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MITGARD (Mitochondrial Genome Assembly from RNA-seq Data) is a computational tool designed to recover the mitochondrial genome from RNA-seq data of any Eukaryote species.<\/p>\n<!-- Time to render link large description section of link id 24674: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MITGARD> How to use <\/a>\n<!-- Time to render notes section of link id 24674: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24674: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/chrishah\/MITObim\" id=\"link-24387\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MITObim<\/a>\n<!-- Time to render name section of link id 24387: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads.<\/p>\n<!-- Time to render link large description section of link id 24387: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MITObim> How to use <\/a>\n<!-- Time to render notes section of link id 24387: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24387: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/RemiAllio\/MitoFinder\" id=\"link-24388\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoFinder<\/a>\n<!-- Time to render name section of link id 24388: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data. MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi\/PacBio\/Nanopore\/Illumina sequencing data...)<\/p>\n<!-- Time to render link large description section of link id 24388: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24388: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24388: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/marcelauliano\/MitoHiFi\" id=\"link-24389\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoHiFi<\/a>\n<!-- Time to render name section of link id 24389: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MitoHiFi circularises, cuts and annotates the mitogenome from contigs assembled with PacBio HiFi reads and softwares such as HiCanu or Hifiasm.<\/p>\n<!-- Time to render link large description section of link id 24389: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoHiFi> How to use <\/a>\n<!-- Time to render notes section of link id 24389: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24389: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/gf777\/mitoVGP\" id=\"link-24391\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mitoVGP<\/a>\n<!-- Time to render name section of link id 24391: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The Vertebrate Genomes Project Mitogenome Assembly Pipeline.<\/p>\n<!-- Time to render link large description section of link id 24391: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24391: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24391: 0.00017309188842773 --> \n<tr><td><a href=\"https:\/\/github.com\/linzhi2013\/MitoZ\" id=\"link-24392\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoZ<\/a>\n<!-- Time to render name section of link id 24392: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization.<\/p>\n<!-- Time to render link large description section of link id 24392: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoZ> How to use <\/a>\n<!-- Time to render notes section of link id 24392: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24392: 0.00012803077697754 --> \n<tr><td><a href=\"https:\/\/github.com\/milaboratory\/mixcr\" id=\"link-24393\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiXCR<\/a>\n<!-- Time to render name section of link id 24393: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24393: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24393: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24393: 0.00010108947753906 --> \n<tr><td><a href=\"https:\/\/github.com\/nunofonseca\/msi\" id=\"link-24399\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MSI<\/a>\n<!-- Time to render name section of link id 24399: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MSI was designed for sequencing reads with higher error rates (e.g., as the ones produced by Nanopore's sequencers) but also works with reads with lower error rates (e.g., Illumina).<\/p>\n<!-- Time to render link large description section of link id 24399: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24399: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24399: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/anne-gcd\/MTG-Link\" id=\"link-24400\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MTG-Link<\/a>\n<!-- Time to render name section of link id 24400: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MTG-Link is a novel gap-filling tool for draft genome assemblies, dedicated to linked read data.<\/p>\n<!-- Time to render link large description section of link id 24400: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24400: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24400: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bluenote-1577\/myloasm\" id=\"link-25993\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">myloasm<\/a>\n<!-- Time to render name section of link id 25993: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Myloasm is a de novo metagenome assembler for long-read sequencing data. It takes sequencing reads and outputs polished contigs in a single command.<\/p>\n<!-- Time to render link large description section of link id 25993: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_myloasm> How to use <\/a>\n<!-- Time to render notes section of link id 25993: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25993: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/jts\/nanopolish\" id=\"link-23823\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Nanopolish<\/a>\n<!-- Time to render name section of link id 23823: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A nanopore consensus algorithm using a signal-level hidden Markov model. Signal-level algorithms for MinION data.<\/p>\n<!-- Time to render link large description section of link id 23823: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Nanopolish> How to use <\/a>\n<!-- Time to render notes section of link id 23823: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23823: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/CarlierLab\/NanoSeq\" id=\"link-25615\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoSeq<\/a>\n<!-- Time to render name section of link id 25615: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pipeline used at the LIPME to assemble plasmid and PCR sequences with Nanopore.<\/p>\n<!-- Time to render link large description section of link id 25615: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoSeq> How to use <\/a>\n<!-- Time to render notes section of link id 25615: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25615: 0.00017809867858887 --> \n<tr><td><a href=\"http:\/\/www.genoscope.cns.fr\/externe\/nas\/\" id=\"link-23990\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NaS<\/a>\n<!-- Time to render name section of link id 23990: 2.8610229492188E-6 --> \n<\/td>\n<td><p>NaS is a hybrid approach developed to take advantage of data generated using MinION device. It combines Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads<\/p>\n<!-- Time to render link large description section of link id 23990: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23990: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23990: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/NECAT\" id=\"link-24411\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NECAT<\/a>\n<!-- Time to render name section of link id 24411: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.<\/p>\n<!-- Time to render link large description section of link id 24411: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NECAT> How to use <\/a>\n<!-- Time to render notes section of link id 24411: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24411: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/en.wikipedia.org\/wiki\/Newbler\" id=\"link-23680\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Newbler<\/a>\n<!-- Time to render name section of link id 23680: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche diagnostic.<\/p>\n<!-- Time to render link large description section of link id 23680: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23680: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23680: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/Nextomics\/NextDenovo\" id=\"link-24414\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NextDenovo<\/a>\n<!-- Time to render name section of link id 24414: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NextDenovo is a string graph-based de novo assembler for TGS long reads.<\/p>\n<!-- Time to render link large description section of link id 24414: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextDenovo> How to use <\/a>\n<!-- Time to render notes section of link id 24414: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24414: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/ndierckx\/NOVOLoci\" id=\"link-26077\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NOVOLoci<\/a>\n<!-- Time to render name section of link id 26077: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NOVOLoci is a haplotype aware assembler for targeted assembly or whole genome assembly of small genomes.\u00a0<\/p>\r\n<p dir=\"auto\">We currently recommend limiting the assembly size to regions &lt;20 Mb in targeted-mode and diploid genomes that are &lt;250 Mb in WG-mode, with a minimum sequencing depth of 10x per haplotype.<\/p>\r\n<p dir=\"auto\">If you do need to phase accuratly and you have HiFi or R10 ONT data, it is adviced to use Hifiasm, as it is has a much shorter runtime.<\/p>\r\n<p>Currently it is only available for Nanopore, PacBio and hybrid options will be available soon.<\/p>\n<!-- Time to render link large description section of link id 26077: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NOVOLoci> How to use <\/a>\n<!-- Time to render notes section of link id 26077: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26077: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/ndierckx\/NOVOPlasty\" id=\"link-24055\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NOVOPlasty<\/a>\n<!-- Time to render name section of link id 24055: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NOVOPlasty is a de novo assembler and variance caller for short circular genomes.<\/p>\n<!-- Time to render link large description section of link id 24055: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NOVOPlasty> How to use <\/a>\n<!-- Time to render notes section of link id 24055: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24055: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/clwgg\/nQuire\" id=\"link-24420\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nQuire<\/a>\n<!-- Time to render name section of link id 24420: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A statistical framework for ploidy estimation using NGS short-read data.<\/p>\n<!-- Time to render link large description section of link id 24420: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_nQuire> How to use <\/a>\n<!-- Time to render notes section of link id 24420: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24420: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ntEdit\" id=\"link-24421\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ntEdit<\/a>\n<!-- Time to render name section of link id 24421: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ntEdit is a fast and scalable genomics application for polishing genome assembly drafts. It simplifies polishing and \"haploidization\" of gene and genome sequences with its re-usable Bloom filter design.<\/p>\n<!-- Time to render link large description section of link id 24421: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24421: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24421: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ntjoin\" id=\"link-24423\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ntJoin<\/a>\n<!-- Time to render name section of link id 24423: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Scaffolding draft assemblies using reference assemblies and minimizer graphs<\/p>\n<!-- Time to render link large description section of link id 24423: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ntJoin> How to use <\/a>\n<!-- Time to render notes section of link id 24423: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24423: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/dzerbino\/oases\" id=\"link-23683\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Oases<\/a>\n<!-- Time to render name section of link id 23683: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz). <br \/>\r\n<br \/>\r\nOases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.<\/p>\n<!-- Time to render link large description section of link id 23683: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Oases> How to use <\/a>\n<!-- Time to render notes section of link id 23683: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23683: 0.00014185905456543 --> \n<tr><td><a href=\"https:\/\/github.com\/c-zhou\/oatk\" id=\"link-25662\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">oatk<\/a>\n<!-- Time to render name section of link id 25662: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A organelle de novo genome assembly toolkit. (Install include OatkDB)<\/p>\n<!-- Time to render link large description section of link id 25662: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Oatk> How to use <\/a>\n<!-- Time to render notes section of link id 25662: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25662: 0.0001380443572998 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/org-asm\/org-asm\" id=\"link-24106\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ORG.asm<\/a>\n<!-- Time to render name section of link id 24106: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The ORGanelle ASseMbler aims to target the assembling of small sequences over-represented in a whole genome shotgun sequence dataset.<\/p>\n<!-- Time to render link large description section of link id 24106: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ORG.Asm> How to use <\/a>\n<!-- Time to render notes section of link id 24106: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24106: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/aubombarely\/Organelle_PBA\" id=\"link-24429\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Organelle_PBA<\/a>\n<!-- Time to render name section of link id 24429: 1.9073486328125E-6 --> \n<\/td>\n<td><p>OrganelleRef_PBA is a script to perform a de-novo PacBio assemblies of any organelle (chloroplast or mitochondrial genomes) using several programs.<\/p>\n<!-- Time to render link large description section of link id 24429: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24429: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24429: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/PASApipeline\/PASApipeline\" id=\"link-23687\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PASApipeline<\/a>\n<!-- Time to render name section of link id 23687: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.<\/p>\n<!-- Time to render link large description section of link id 23687: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PASApipeline> How to use <\/a>\n<!-- Time to render notes section of link id 23687: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23687: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbbioconda\" id=\"link-23992\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pb-assembly<\/a>\n<!-- Time to render name section of link id 23992: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PacBio\u00ae tools\u00a0 :\u00a0 everything needed to run Falcon and Unzip<\/p>\n<!-- Time to render link large description section of link id 23992: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23992: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23992: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/lemene\/PECAT\" id=\"link-25450\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PECAT<\/a>\n<!-- Time to render name section of link id 25450: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PECAT is a phased error correction and assembly tool for long reads. It includes a haplotype-aware correction method and an efficient diploid assembly method.<\/p>\n<!-- Time to render link large description section of link id 25450: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PECAT> How to use <\/a>\n<!-- Time to render notes section of link id 25450: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25450: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/cschin\/peregrine-2021\" id=\"link-24093\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Peregrine<\/a>\n<!-- Time to render name section of link id 24093: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Peregrine is a fast genome assembler for accurate long reads (length &gt; 10kb, accuraccy &gt; 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus.<\/p>\n<!-- Time to render link large description section of link id 24093: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Peregrine> How to use <\/a>\n<!-- Time to render notes section of link id 24093: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24093: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/phasebook\/phasebook\" id=\"link-24439\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phasebook<\/a>\n<!-- Time to render name section of link id 24439: 1.9073486328125E-6 --> \n<\/td>\n<td><p>phasebook is a novel approach for reconstructing the haplotypes of diploid genomes from long reads de novo, that is without the need for a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24439: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24439: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24439: 0.0001380443572998 --> \n<tr><td><a href=\"https:\/\/github.com\/broadinstitute\/pilon\" id=\"link-23821\" class=\"track_this_link \" rel=\"noopener noreferrer\">Pilon<\/a>\n<!-- Time to render name section of link id 23821: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pilon is an automated genome assembly improvement and variant detection tool.<\/p>\n<!-- Time to render link large description section of link id 23821: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pilon> How to use <\/a>\n<!-- Time to render notes section of link id 23821: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23821: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/leaemiliepradier\/PlasForest\" id=\"link-24451\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlasForest<\/a>\n<!-- Time to render name section of link id 24451: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A random forest classifier of contigs to identify contigs of plasmid origin in contig and scaffold genomes.<\/p>\n<!-- Time to render link large description section of link id 24451: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlasForest> How to use <\/a>\n<!-- Time to render notes section of link id 24451: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24451: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/plass\" id=\"link-24703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Plass<\/a>\n<!-- Time to render name section of link id 24703: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.<\/p>\n<!-- Time to render link large description section of link id 24703: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24703: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24703: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/gbouras13\/plassembler\" id=\"link-25474\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">plassembler<\/a>\n<!-- Time to render name section of link id 25474: 2.1457672119141E-6 --> \n<\/td>\n<td><p>plassembler is a program that is designed for automated &amp; fast assembly of plasmids in bacterial genomes that have been hybrid sequenced with long read &amp; paired-end short read sequencing.<\/p>\n<!-- Time to render link large description section of link id 25474: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_plassembler> How to use <\/a>\n<!-- Time to render notes section of link id 25474: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25474: 0.00011205673217773 --> \n<tr><td><a href=\"http:\/\/platanus.bio.titech.ac.jp\/platanus-assembler\" id=\"link-24453\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Platanus<\/a>\n<!-- Time to render name section of link id 24453: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24453: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24453: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24453: 0.00011706352233887 --> \n<tr><td><a href=\"http:\/\/platanus.bio.titech.ac.jp\/platanus2\" id=\"link-24455\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Platanus2<\/a>\n<!-- Time to render name section of link id 24455: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Platanus-allee (Platanus2) is a de novo haplotype assembler (phasing tool), which assembles each haplotype sequence in a diploid genome.<\/p>\n<!-- Time to render link large description section of link id 24455: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24455: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24455: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/schneebergerlab\/plotsr\" id=\"link-24456\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">plotsr<\/a>\n<!-- Time to render name section of link id 24456: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tool to plot synteny and structural rearrangements between genomes.<\/p>\n<!-- Time to render link large description section of link id 24456: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_plotsr> How to use <\/a>\n<!-- Time to render notes section of link id 24456: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24456: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Polypolish\" id=\"link-24457\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Polypolish<\/a>\n<!-- Time to render name section of link id 24457: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Polypolish is a tool for polishing genome assemblies with short reads.<\/p>\n<!-- Time to render link large description section of link id 24457: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Polypolish> How to use <\/a>\n<!-- Time to render notes section of link id 24457: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24457: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/dfguan\/purge_dups\" id=\"link-24469\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Purge_Dups<\/a>\n<!-- Time to render name section of link id 24469: 2.8610229492188E-6 --> \n<\/td>\n<td><p>purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.<\/p>\n<!-- Time to render link large description section of link id 24469: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Purge_Dups> How to use <\/a>\n<!-- Time to render notes section of link id 24469: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24469: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/mroachawri\/purge_haplotigs\" id=\"link-24051\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Purge_Haplotigs<\/a>\n<!-- Time to render name section of link id 24051: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pipeline to help with curating heterozygous diploid genome assemblies (for instance when assembling using FALCON or FALCON-unzip).<\/p>\n<!-- Time to render link large description section of link id 24051: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24051: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24051: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/gbouras13\/pypolca\" id=\"link-25451\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pypolca<\/a>\n<!-- Time to render name section of link id 25451: 1.9073486328125E-6 --> \n<\/td>\n<td><p>pypolca is a Standalone Python re-implementation of the POLCA polisher from the MaSuRCA genome assembly and analysis toolkit.<\/p>\n<!-- Time to render link large description section of link id 25451: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pypolca> How to use <\/a>\n<!-- Time to render notes section of link id 25451: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25451: 0.0001370906829834 --> \n<tr><td><a href=\"https:\/\/github.com\/aaranyue\/quarTeT\" id=\"link-25192\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quarTeT<\/a>\n<!-- Time to render name section of link id 25192: 1.9073486328125E-6 --> \n<\/td>\n<td><p>quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.<\/p>\n<!-- Time to render link large description section of link id 25192: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_quarTeT> How to use <\/a>\n<!-- Time to render notes section of link id 25192: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25192: 0.00012898445129395 --> \n<tr><td><a href=\"https:\/\/quast.sourceforge.net\" id=\"link-23706\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">QUAST<\/a>\n<!-- Time to render name section of link id 23706: 1.9073486328125E-6 --> \n<\/td>\n<td><p>QUAST evaluates genome assemblies by computing various metrics<\/p>\n<!-- Time to render link large description section of link id 23706: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_QUAST> How to use <\/a>\n<!-- Time to render notes section of link id 23706: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23706: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/mahulchak\/quickmerge\" id=\"link-23938\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quickmerge<\/a>\n<!-- Time to render name section of link id 23938: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies<\/p>\n<!-- Time to render link large description section of link id 23938: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23938: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23938: 0.00012683868408203 --> \n<tr><td><a href=\"https:\/\/github.com\/lbcb-sci\/ra\" id=\"link-23949\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ra<\/a>\n<!-- Time to render name section of link id 23949: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Ra is as a fast and easy to use assembler for raw reads generated by third generation sequencing.<\/p>\n<!-- Time to render link large description section of link id 23949: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23949: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23949: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Rebaler\" id=\"link-24478\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Rabaler<\/a>\n<!-- Time to render name section of link id 24478: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences.<\/p>\n<!-- Time to render link large description section of link id 24478: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24478: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24478: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/lbcb-sci\/racon\" id=\"link-23828\" class=\"track_this_link \" rel=\"noopener noreferrer\">Racon<\/a>\n<!-- Time to render name section of link id 23828: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Consensus module for raw de novo DNA assembly of long uncorrected reads.<\/p>\n<!-- Time to render link large description section of link id 23828: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Racon> How to use <\/a>\n<!-- Time to render notes section of link id 23828: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23828: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/at-cg\/RAFT\" id=\"link-25101\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAFT<\/a>\n<!-- Time to render name section of link id 25101: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RAFT (Repeat Aware Fragmentation Tool) is an algorithm designed to improve assembly quality by rescuing contained reads.<\/p>\r\n<p dir=\"auto\">RAFT breaks long reads into smaller sub-reads by following an algorithm described in our <a href=\"https:\/\/github.com\/at-cg\/RAFT#papers\">preprint<\/a>. The read fragmentation allows an OLC assembler to retain contained reads during string graph construction. When input reads have non-uniform lengths, retaining contained reads improves assembly contiguity and base-level accuracy. The inputs to RAFT include an error-corrected read file in FASTA\/FASTQ format and an all-vs-all alignment file in PAF format. It performs read fragmentation and outputs the fragmented reads in FASTA format.<\/p>\r\n<p dir=\"auto\">We recommend users to use\u00a0<a href=\"https:\/\/github.com\/chhylp123\/hifiasm\">hifiasm<\/a>\u00a0for the initial steps (read error correction, all-vs-all overlap computation) and also for the final step (assembly of fragmented reads). The assembly output format of hifiasm is described\u00a0<a href=\"https:\/\/hifiasm.readthedocs.io\/en\/latest\/interpreting-output.html#interpreting-output\" rel=\"nofollow\">here<\/a>.<\/p>\r\n<p dir=\"auto\"><em>The RAFT-hifiasm workflow is recommended for long accurate reads with non-uniform length distribution (e.g., ONT Duplex, or a mixture of ONT Duplex and HiFi reads). ONT UL reads can optionally be\u00a0<a href=\"https:\/\/github.com\/chhylp123\/hifiasm#ul\">integrated<\/a>\u00a0during the final assembly step.<\/em><\/p>\n<!-- Time to render link large description section of link id 25101: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAFT> How to use <\/a>\n<!-- Time to render notes section of link id 25101: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25101: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/malonge\/RaGOO\" id=\"link-24045\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RaGOO<\/a>\n<!-- Time to render name section of link id 24045: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24045: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24045: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24045: 0.0001068115234375 --> \n<tr><td><a href=\"http:\/\/fenderglass.github.io\/Ragout\/\" id=\"link-23951\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ragout<\/a>\n<!-- Time to render name section of link id 23951: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references.<\/p>\n<!-- Time to render link large description section of link id 23951: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23951: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23951: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/malonge\/RagTag\" id=\"link-24481\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RagTag<\/a>\n<!-- Time to render name section of link id 24481: 1.1205673217773E-5 --> \n<\/td>\n<td><p>RagTag, the successor to RaGOO, is a command line tool for reference-guided genome assembly improvement.<\/p>\n<!-- Time to render link large description section of link id 24481: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RagTag> How to use <\/a>\n<!-- Time to render notes section of link id 24481: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24481: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/TGAC\/RAMPART\" id=\"link-24483\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAMPART<\/a>\n<!-- Time to render name section of link id 24483: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RAMPART is a configurable pipeline for de novo assembly of DNA sequence data. RAMPART is not a de novo assembler.<\/p>\n<!-- Time to render link large description section of link id 24483: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24483: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24483: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/moeinzadeh\/Ranbow\" id=\"link-24484\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ranbow<\/a>\n<!-- Time to render name section of link id 24484: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Ranbow is a haplotype assembler for polyploid genomes.<\/p>\n<!-- Time to render link large description section of link id 24484: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24484: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24484: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/Ratatosk\" id=\"link-24485\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ratatosk<\/a>\n<!-- Time to render name section of link id 24485: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ratatosk is a phased error correction tool for erroneous long reads based on compacted and colored de Bruijn graphs built from accurate short reads.<\/p>\n<!-- Time to render link large description section of link id 24485: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24485: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24485: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/lbcb-sci\/raven\" id=\"link-24486\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Raven<\/a>\n<!-- Time to render name section of link id 24486: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Raven is a de novo genome assembler for long uncorrected reads.<\/p>\n<!-- Time to render link large description section of link id 24486: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Raven> How to use <\/a>\n<!-- Time to render notes section of link id 24486: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24486: 0.00017499923706055 --> \n<tr><td><a href=\"http:\/\/denovoassembler.sourceforge.net\/download.html\" id=\"link-23709\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ray<\/a>\n<!-- Time to render name section of link id 23709: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assemble genomes in parallel using the message-passing interface<\/p>\n<!-- Time to render link large description section of link id 23709: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23709: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23709: 0.00011491775512695 --> \n<tr><td><a href=\"http:\/\/www.sanger.ac.uk\/resources\/software\/reapr\/#t_2)\" id=\"link-23713\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REAPR<\/a>\n<!-- Time to render name section of link id 23713: 2.1457672119141E-6 --> \n<\/td>\n<td><p>REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.<\/p>\n<!-- Time to render link large description section of link id 23713: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23713: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23713: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/lpryszcz\/redundans\" id=\"link-23840\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Redundans<\/a>\n<!-- Time to render name section of link id 23840: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Redundans is a pipeline that assists an assembly of heterozygous\/polymorphic genomes.<\/p>\n<!-- Time to render link large description section of link id 23840: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23840: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23840: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/cpouchon\/REFMAKER\" id=\"link-25264\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REFMAKER<\/a>\n<!-- Time to render name section of link id 25264: 1.9073486328125E-6 --> \n<\/td>\n<td><p>REFMAKER is a command-line and user-friendly pipeline providing different tools to create nuclear references from genomic assemblies of shotgun libraries.<\/p>\n<!-- Time to render link large description section of link id 25264: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REFMAKER> How to use <\/a>\n<!-- Time to render notes section of link id 25264: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25264: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/simoncchu\/REPdenovo\" id=\"link-24491\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REPdenovo<\/a>\n<!-- Time to render name section of link id 24491: 2.1457672119141E-6 --> \n<\/td>\n<td><p>REPdenovo is designed for constructing repeats directly from sequence (paired-end) reads. It based on the idea of frequent k-mer assembly. REPdenovo provides many functionalities, and can generate much longer repeats than existing tools. Internally, REPdenovo uses Jellyfish for k-mer counting, Velvet for assembly, and bwa to map reads on the Transposable Elements.<\/p>\n<!-- Time to render link large description section of link id 24491: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24491: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24491: 0.00015115737915039 --> \n<tr><td><a href=\"https:\/\/github.com\/nickp60\/riboSeed\" id=\"link-25200\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">riboSeed<\/a>\n<!-- Time to render name section of link id 25200: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Pipeline for using ribosomal flanking regions to improve bacterial genome assembly.<\/p>\n<!-- Time to render link large description section of link id 25200: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_riboSeed> How to use <\/a>\n<!-- Time to render notes section of link id 25200: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25200: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/AppliedBioinformatics\/runBNG\" id=\"link-24872\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">runBNG<\/a>\n<!-- Time to render name section of link id 24872: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An easy way to run BioNano genomic analysis.<\/p>\n<!-- Time to render link large description section of link id 24872: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24872: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24872: 0.00017213821411133 --> \n<tr><td><a href=\"https:\/\/github.com\/ekimb\/rust-mdbg\" id=\"link-24506\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rust-mdbg<\/a>\n<!-- Time to render name section of link id 24506: 3.0994415283203E-6 --> \n<\/td>\n<td><p>rust-mdbg is an ultra-fast minimizer-space de Bruijn graph (mdBG) implementation, geared towards the assembly of long and accurate reads such as PacBio HiFi.<\/p>\n<!-- Time to render link large description section of link id 24506: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rust-mdbg> How to use <\/a>\n<!-- Time to render notes section of link id 24506: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24506: 0.00012588500976562 --> \n<tr><td><a href=\"https:\/\/github.com\/machinegun\/SALSA\" id=\"link-24109\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SALSA<\/a>\n<!-- Time to render name section of link id 24109: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool to scaffold long read assemblies with Hi-C data<\/p>\n<!-- Time to render link large description section of link id 24109: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SALSA> How to use <\/a>\n<!-- Time to render notes section of link id 24109: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24109: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/wtsi-hpag\/Scaff10X\" id=\"link-24510\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scaff10X<\/a>\n<!-- Time to render name section of link id 24510: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads<\/p>\n<!-- Time to render link large description section of link id 24510: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24510: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24510: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/Kingsford-Group\/scallop\" id=\"link-24873\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scallop<\/a>\n<!-- Time to render name section of link id 24873: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Scallop is an accurate reference-based transcript assembler.<\/p>\n<!-- Time to render link large description section of link id 24873: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Scallop> How to use <\/a>\n<!-- Time to render notes section of link id 24873: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24873: 0.00020599365234375 --> \n<tr><td><a href=\"https:\/\/github.com\/mvollger\/SDA\" id=\"link-24052\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SDA<\/a>\n<!-- Time to render name section of link id 24052: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Segmental Duplication Assembler<\/p>\n<!-- Time to render link large description section of link id 24052: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24052: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24052: 0.00013589859008789 --> \n<tr><td><a href=\"https:\/\/github.com\/AntonelliLab\/seqcap_processor\" id=\"link-24513\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SECAPR<\/a>\n<!-- Time to render name section of link id 24513: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Used to process targeted sequencing (or Gene capture) data by applying assembly and subsequent mapping algorithms (reducing paralogs unlike Hybpiper).<\/p>\n<!-- Time to render link large description section of link id 24513: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24513: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24513: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/jts\/sga\" id=\"link-23726\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SGA<\/a>\n<!-- Time to render name section of link id 23726: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.<\/p>\n<!-- Time to render link large description section of link id 23726: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23726: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23726: 0.00012421607971191 --> \n<tr><td><a href=\"https:\/\/github.com\/paoloshasta\/shasta\" id=\"link-24118\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Shasta<\/a>\n<!-- Time to render name section of link id 24118: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.<\/p>\n<!-- Time to render link large description section of link id 24118: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Shasta> How to use <\/a>\n<!-- Time to render notes section of link id 24118: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24118: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/ChrisHIV\/shiver\" id=\"link-24670\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">shiver<\/a>\n<!-- Time to render name section of link id 24670: 2.1457672119141E-6 --> \n<\/td>\n<td><p>shiver is a tool for mapping paired-end short reads to a custom reference sequence constructed using do novo assembled contigs, in order to minimise the biased loss of information that occurs from mapping to a reference that differs from the sample.<\/p>\n<!-- Time to render link large description section of link id 24670: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24670: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24670: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/a\/ucr.edu\/slicembler\/home\" id=\"link-24520\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLICEMBLER<\/a>\n<!-- Time to render name section of link id 24520: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SLICEMBLER is a meta-assembler designed for ultra-deep sequencing data\/<\/p>\n<!-- Time to render link large description section of link id 24520: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24520: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24520: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/SLR-superscaffolder\" id=\"link-24521\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLR-superscaffolder<\/a>\n<!-- Time to render name section of link id 24521: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is a scaffold assembler designed for stLFR reads. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds.<\/p>\n<!-- Time to render link large description section of link id 24521: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24521: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24521: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/ruanjue\/smartdenovo\" id=\"link-23845\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">smartdenovo<\/a>\n<!-- Time to render name section of link id 23845: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.<\/p>\n<!-- Time to render link large description section of link id 23845: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_smartdenovo> How to use <\/a>\n<!-- Time to render notes section of link id 23845: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23845: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/www.pacb.com\/support\/software-downloads\/\" id=\"link-23904\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SMRTLink<\/a>\n<!-- Time to render name section of link id 23904: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SMRT Link is the web-based end-to-end workflow manager for the Sequel\u2122 System. (installed in mode command line on our cluster)<\/p>\n<!-- Time to render link large description section of link id 23904: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SMRTLink> How to use <\/a>\n<!-- Time to render notes section of link id 23904: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23904: 0.00012683868408203 --> \n<tr><td><a href=\"https:\/\/github.com\/gigascience\/bgi-soap2\/tree\/master\/tools\/soap.coverage\/2.7.7\" id=\"link-24526\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">soap.coverage<\/a>\n<!-- Time to render name section of link id 24526: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Can calculate sequencing coverage or physical coverage as well as duplication rate and details of specific block for each segments and whole genome by using SOAP, Blat, Blast, BlastZ, mummer and MAQ aligement results with multi-thread. Gzip file supported.<\/p>\n<!-- Time to render link large description section of link id 24526: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24526: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24526: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/soap.genomics.org.cn\/soapdenovo.html\" id=\"link-23733\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SOAPdenovo<\/a>\n<!-- Time to render name section of link id 23733: 3.0994415283203E-6 --> \n<\/td>\n<td><div class=\"title\">ttSOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. <b><br \/>\r\n<\/b><\/div>\n<!-- Time to render link large description section of link id 23733: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23733: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23733: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/aquaskyline\/SOAPdenovo-Trans\" id=\"link-24527\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SOAPdenovo-Trans<\/a>\n<!-- Time to render name section of link id 24527: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.<\/p>\n<!-- Time to render link large description section of link id 24527: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24527: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24527: 0.00013899803161621 --> \n<tr><td><a href=\"http:\/\/cab.spbu.ru\/software\/spades\/\" id=\"link-23735\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SPAdes<\/a>\n<!-- Time to render name section of link id 23735: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SPAdes \uff96 St. Petersburg genome assembler \uff96 is intended for both standard isolates and single-cell MDA bacteria assemblies.<\/p>\n<!-- Time to render link large description section of link id 23735: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SPAdes> How to use <\/a>\n<!-- Time to render notes section of link id 23735: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23735: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/BrendelGroup\/SRAssembler\" id=\"link-24540\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SRAsembler<\/a>\n<!-- Time to render name section of link id 24540: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SRAssembler (Selective Recursive local Assembler) is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologous to a query DNA or protein sequence.<\/p>\n<!-- Time to render link large description section of link id 24540: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24540: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24540: 0.00012302398681641 --> \n<tr><td><a href=\"http:\/\/www.baseclear.com\/lab-products\/bioinformatics-tools\/sspace-standard\/\" id=\"link-23737\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SSPACE<\/a>\n<!-- Time to render name section of link id 23737: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS\u00a0 paired-read data.<\/p>\n<!-- Time to render link large description section of link id 23737: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23737: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23737: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.baseclear.com\/genomics\/bioinformatics\/basetools\/SSPACE_longread\" id=\"link-23738\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SSPACE-LongRead<\/a>\n<!-- Time to render name section of link id 23738: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads).<\/p>\n<!-- Time to render link large description section of link id 23738: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23738: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23738: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/stringtie\" id=\"link-23741\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">StringTie<\/a>\n<!-- Time to render name section of link id 23741: 1.9073486328125E-6 --> \n<\/td>\n<td><p><b>StringTie<\/b> is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional <i>de novo<\/i> assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.<\/p>\n<!-- Time to render link large description section of link id 23741: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_StringTie> How to use <\/a>\n<!-- Time to render notes section of link id 23741: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23741: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/support.10xgenomics.com\/de-novo-assembly\/software\/overview\/welcome\" id=\"link-23813\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Supernova<\/a>\n<!-- Time to render name section of link id 23813: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source.<\/p>\n<!-- Time to render link large description section of link id 23813: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23813: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23813: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/deepomicslab\/SuperTAD\" id=\"link-24549\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SuperTAD<\/a>\n<!-- Time to render name section of link id 24549: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SuperTAD is an open-source command-line TAD detection package written in C++. It takes either raw or normalized Hi-C contact maps as inputs.<\/p>\n<!-- Time to render link large description section of link id 24549: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SuperTAD> How to use <\/a>\n<!-- Time to render notes section of link id 24549: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24549: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/tacorna\/taco\" id=\"link-25534\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TACO<\/a>\n<!-- Time to render name section of link id 25534: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Multi-sample transcriptome assembly from RNA-Seq.<\/p>\n<!-- Time to render link large description section of link id 25534: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TACO> How to use <\/a>\n<!-- Time to render notes section of link id 25534: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25534: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/johnomics\/tapestry\" id=\"link-24094\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tapestry<\/a>\n<!-- Time to render name section of link id 24094: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tapestry is a tool to validate and edit small eukaryotic genome assemblies using long sequence reads. It is designed to help identify complete chromosomes, symbionts, haplotypes, complex features and errors in close-to-complete genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24094: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24094: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24094: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/tgicl\/\" id=\"link-23609\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TGICL<\/a>\n<!-- Time to render name section of link id 23609: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This package automates clustering and assembly of a large EST\/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's<i> megablast <\/i>, and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3.<\/p>\n<!-- Time to render link large description section of link id 23609: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TGICL> How to use <\/a>\n<!-- Time to render notes section of link id 23609: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23609: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/TGSGapFiller\" id=\"link-24562\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TGSGapFiller<\/a>\n<!-- Time to render name section of link id 24562: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A gap filling tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.<\/p>\n<!-- Time to render link large description section of link id 24562: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24562: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24562: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/bcgsc.github.io\/tigmint\/\" id=\"link-23962\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tigmint<\/a>\n<!-- Time to render name section of link id 23962: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tigmint identifies and corrects misassemblies using linked reads from 10x Genomics Chromium.<\/p>\n<!-- Time to render link large description section of link id 23962: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23962: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23962: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/hibberdlab.com\/transrate\/index.html\" id=\"link-23775\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Transrate<\/a>\n<!-- Time to render name section of link id 23775: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Transrate is software for de-novo transcriptome assembly quality analysis.<\/p>\n<!-- Time to render link large description section of link id 23775: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Transrate> How to use <\/a>\n<!-- Time to render notes section of link id 23775: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23775: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/trinityrnaseq.sourceforge.net\/\" id=\"link-23755\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">trinityrnaseq<\/a>\n<!-- Time to render name section of link id 23755: 2.1457672119141E-6 --> \n<\/td>\n<td><div class=\"para\">Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.<\/div>\n<!-- Time to render link large description section of link id 23755: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_trinityrnaseq> How to use <\/a>\n<!-- Time to render notes section of link id 23755: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23755: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Trycycler\" id=\"link-24571\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trycycler<\/a>\n<!-- Time to render name section of link id 24571: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 24571: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Trycycler> How to use <\/a>\n<!-- Time to render notes section of link id 24571: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24571: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Unicycler\" id=\"link-23948\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Unicycler<\/a>\n<!-- Time to render name section of link id 23948: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Unicycler is an assembly pipeline for bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 23948: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Unicycler> How to use <\/a>\n<!-- Time to render notes section of link id 23948: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23948: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/unimap\" id=\"link-24822\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Unimap<\/a>\n<!-- Time to render name section of link id 24822: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment.<\/p>\n<!-- Time to render link large description section of link id 24822: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Unimap> How to use <\/a>\n<!-- Time to render notes section of link id 24822: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24822: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/dzerbino\/velvet\" id=\"link-23761\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Velvet<\/a>\n<!-- Time to render name section of link id 23761: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. <br \/>\r\n<br \/>\r\nVelvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.<\/p>\n<!-- Time to render link large description section of link id 23761: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Velvet> How to use <\/a>\n<!-- Time to render notes section of link id 23761: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23761: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/verkko\" id=\"link-24580\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Verkko<\/a>\n<!-- Time to render name section of link id 24580: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads.<\/p>\n<!-- Time to render link large description section of link id 24580: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Verkko> How to use <\/a>\n<!-- Time to render notes section of link id 24580: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24580: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/jjuhyunkim\/verkko-fillet\" id=\"link-26115\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">verkko-fillet<\/a>\n<!-- Time to render name section of link id 26115: 1.9073486328125E-6 --> \n<\/td>\n<td><p>verkko-fillet is an easy-to-use toolkit for cleaning Verkko assemblies.<\/p>\n<!-- Time to render link large description section of link id 26115: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_verkko-fillet> How to use <\/a>\n<!-- Time to render notes section of link id 26115: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26115: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/www.tbi.univie.ac.at\/RNA\/#\" id=\"link-23762\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViennaRNA<\/a>\n<!-- Time to render name section of link id 23762: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Vienna RNA package allows RNA Secondary Structure Prediction and Comparison<\/p>\n<!-- Time to render link large description section of link id 23762: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ViennaRNA> How to use <\/a>\n<!-- Time to render notes section of link id 23762: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23762: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/viquas\/\" id=\"link-24583\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViQuaS<\/a>\n<!-- Time to render name section of link id 24583: 2.8610229492188E-6 --> \n<\/td>\n<td><p>An improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing.<\/p>\n<!-- Time to render link large description section of link id 24583: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24583: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24583: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/adigenova\/wengan\" id=\"link-24587\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Wengan<\/a>\n<!-- Time to render name section of link id 24587: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An accurate and ultra-fast genome assembler<\/p>\n<!-- Time to render link large description section of link id 24587: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24587: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24587: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/arzwa\/wgd\" id=\"link-24098\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wgd<\/a>\n<!-- Time to render name section of link id 24098: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python package and CLI for whole genome duplication analyse<\/p>\n<!-- Time to render link large description section of link id 24098: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_wgd> How to use <\/a>\n<!-- Time to render notes section of link id 24098: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24098: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/wgs-assembler\/\" id=\"link-24590\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WGS-Assembler<\/a>\n<!-- Time to render name section of link id 24590: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.<\/p>\n<!-- Time to render link large description section of link id 24590: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24590: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24590: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/ruanjue\/wtdbg2\" id=\"link-23999\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wtdbg<\/a>\n<!-- Time to render name section of link id 23999: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT).<\/p>\n<!-- Time to render link large description section of link id 23999: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_wtdbg> How to use <\/a>\n<!-- Time to render notes section of link id 23999: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23999: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/c-zhou\/yahs\" id=\"link-24597\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">YaHS<\/a>\n<!-- Time to render name section of link id 24597: 2.1457672119141E-6 --> \n<\/td>\n<td><p>YaHS is a scaffolding tool using Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 24597: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_YaHS> How to use <\/a>\n<!-- Time to render notes section of link id 24597: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24597: 0.00017690658569336 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => 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class=\"LinkLibraryCat LinkLibraryCat1144 level0\"><!-- Div Category --><div id=\"atac-seq\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">ATAC-Seq<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell-multiome-atac-gex\/software\/overview\/welcome\" id=\"link-24173\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger ARC<\/a>\n<!-- Time to render name section of link id 24173: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cell Ranger ARC's pipelines analyze sequencing data produced from Chromium Single Cell Multiome ATAC + Gene Expression.<\/p>\n<!-- Time to render link large description section of link id 24173: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRangerARC> How to use <\/a>\n<!-- Time to render notes section of link id 24173: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24173: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell-atac\/software\/pipelines\/latest\/what-is-cell-ranger-atac\" id=\"link-24059\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger ATAC<\/a>\n<!-- Time to render name section of link id 24059: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.<\/p>\n<!-- Time to render link large description section of link id 24059: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRangerATAC> How to use <\/a>\n<!-- Time to render notes section of link id 24059: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24059: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/git.embl.de\/grp-zaugg\/diffTF\" id=\"link-25244\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">diffTF<\/a>\n<!-- Time to render name section of link id 25244: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressor.<\/p>\n<!-- Time to render link large description section of link id 25244: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_diffTF> How to use <\/a>\n<!-- Time to render notes section of link id 25244: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25244: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/GreenleafLab\/NucleoATAC\" id=\"link-25500\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NucleoATAC<\/a>\n<!-- Time to render name section of link id 25500: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Python package for calling nucleosomes using ATAC-seq data. Also includes general scripts for working with paired-end ATAC-seq data (or potentially other paired-end data).<\/p>\n<!-- Time to render link large description section of link id 25500: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NucleoATAC> How to use <\/a>\n<!-- Time to render notes section of link id 25500: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25500: 0.00018692016601562 --> \n<tr><td><a href=\"http:\/\/younglab.wi.mit.edu\/super_enhancer_code.html\" id=\"link-24504\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ROSE<\/a>\n<!-- Time to render name section of link id 24504: 1.9073486328125E-6 --> \n<\/td>\n<td><p>To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)<\/p>\n<!-- Time to render link large description section of link id 24504: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ROSE> How to use <\/a>\n<!-- Time to render notes section of link id 24504: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24504: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/guertinlab\/Tn5bias\" id=\"link-26135\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqOutATACBias<\/a>\n<!-- Time to render name section of link id 26135: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A CLI that corrects the sequence bias of Tn5 transposase in ATAC-seq data using a rule ensemble model.<\/p>\n<!-- Time to render link large description section of link id 26135: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqOutATACBias> How to use <\/a>\n<!-- Time to render notes section of link id 26135: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26135: 0.0001838207244873 --> \n<tr><td><a href=\"https:\/\/github.com\/loosolab\/TOBIAS\" id=\"link-24565\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TOBIAS<\/a>\n<!-- Time to render name section of link id 24565: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.<\/p>\n<!-- Time to render link large description section of link id 24565: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TOBIAS> How to use <\/a>\n<!-- Time to render notes section of link id 24565: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24565: 0.00011515617370605 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n           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[thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00090408325195312-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1134 level0\"><!-- Div Category --><div id=\"bs-seq-analysis\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">BS-seq analysis<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/udall-lab.byu.edu\/Research\/Software\/BamBam.aspx\" id=\"link-23922\" class=\"track_this_link \" rel=\"noopener noreferrer\">BamBam<\/a>\n<!-- Time to render name section of link id 23922: 1.9073486328125E-6 --> \n<\/td>\n<td><p>several simple-to-use tools to facilitate NGS analysis<\/p>\n<!-- Time to render link large description section of link id 23922: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23922: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23922: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/huishenlab.github.io\/biscuit\/\" id=\"link-25356\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BISCUIT<\/a>\n<!-- Time to render name section of link id 25356: 2.8610229492188E-6 --> \n<\/td>\n<td><p>BISulfite-seq CUI Toolkit (BISCUIT) is a utility for analyzing sodium bisulfite conversion-based DNA methylation\/modification data.<\/p>\n<!-- Time to render link large description section of link id 25356: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BISCUIT> How to use <\/a>\n<!-- Time to render notes section of link id 25356: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25356: 0.00012493133544922 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/bismark\/\" id=\"link-23597\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bismark<\/a>\n<!-- Time to render name section of link id 23597: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool to map bisulfite converted sequence reads and determine cytosine methylation states<\/p>\n<!-- Time to render link large description section of link id 23597: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bismark> How to use <\/a>\n<!-- Time to render notes section of link id 23597: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23597: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/dnaase\/Bis-tools\" id=\"link-24161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BisSNP<\/a>\n<!-- Time to render name section of link id 24161: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Accurate combined SNP\/Methylation calling.<\/p>\n<!-- Time to render link large description section of link id 24161: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24161: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24161: 0.00011920928955078 --> \n<tr><td><a href=\"http:\/\/pellegrini-legacy.mcdb.ucla.edu\/bs_seeker2\/\" id=\"link-24165\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BS-Seeker2-<\/a>\n<!-- Time to render name section of link id 24165: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.<\/p>\n<!-- Time to render link large description section of link id 24165: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24165: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24165: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/hellbelly\/BS-Snper\" id=\"link-24166\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BS-SNPer<\/a>\n<!-- Time to render name section of link id 24166: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BS-SNPer is an ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM\/SAM format using approximate Bayesian modeling.<\/p>\n<!-- Time to render link large description section of link id 24166: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24166: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24166: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/code.google.com\/p\/bsmap\/\" id=\"link-23602\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BSMAP<\/a>\n<!-- Time to render name section of link id 23602: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference<\/p>\n<!-- Time to render link large description section of link id 23602: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23602: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23602: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/brentp\/bwa-meth\" id=\"link-24169\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwa-meth<\/a>\n<!-- Time to render name section of link id 24169: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.<\/p>\n<!-- Time to render link large description section of link id 24169: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bwa-meth> How to use <\/a>\n<!-- Time to render notes section of link id 24169: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24169: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/Computomics\/\" id=\"link-24711\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MethylScore<\/a>\n<!-- Time to render name section of link id 24711: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Identification of differentially methylated regions between multiple epigenomes from BS-treated read mappings via methylated region calling.<\/p>\n<!-- Time to render link large description section of link id 24711: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MethylScore> How to use <\/a>\n<!-- Time to render notes section of link id 24711: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24711: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/nf-core\/\" id=\"link-24009\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nf-core workflows<\/a>\n<!-- Time to render name section of link id 24009: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This module provide access to workflows nf-core, there are automatically downloaded into your home.<\/p>\r\n<p><strong>More info at <a href=\"https:\/\/github.com\/nf-core\/configs\/blob\/master\/docs\/genotoul.md\">nf-core\/config<\/a> page.<\/strong><\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 24009: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextflowWorkflows> How to use <\/a>\n<!-- Time to render notes section of link id 24009: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24009: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/bsblabludwig\/rastair\/src\/master\/\" id=\"link-25551\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rastair<\/a>\n<!-- Time to render name section of link id 25551: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Fast processing of TET-assisted pyridine borane sequencing (TAPS)-based sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25551: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rastair> How to use <\/a>\n<!-- Time to render notes section of link id 25551: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25551: 0.00011181831359863 --> \n<tr><td><a href=\"https:\/\/www.bioinf.uni-leipzig.de\/Software\/segemehl\/\" id=\"link-24677\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">segemehl<\/a>\n<!-- Time to render name section of link id 24677: 1.9073486328125E-6 --> \n<\/td>\n<td><p>segemehl is a software to map short sequencer reads to reference genomes. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).<\/p>\n<!-- Time to render link large description section of link id 24677: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24677: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24677: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/\" id=\"link-23752\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trim Galore<\/a>\n<!-- Time to render name section of link id 23752: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.<\/p>\n<!-- Time to render link large description section of link id 23752: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TrimGalore> How to use <\/a>\n<!-- Time to render notes section of link id 23752: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23752: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/xie186\/ViewBS\" id=\"link-24582\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViewBS<\/a>\n<!-- Time to render name section of link id 24582: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A powerful toolkit for visualization of high-throughput bisulfite sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24582: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ViewBS> How to use <\/a>\n<!-- Time to render notes section of link id 24582: 0 --> \n<\/td><\/tr>\n<!-- Time to 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0.00085806846618652-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1131 level0\"><!-- Div Category --><div id=\"chip-seq-analysis\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">ChIP-seq analysis<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/tobiasrausch\/alfred\" id=\"link-23978\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Alfred<\/a>\n<!-- Time to render name section of link id 23978: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BAM Statistics, Feature Counting and Annotation<\/p>\n<!-- Time to render link large description section of link id 23978: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23978: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23978: 0.00011897087097168 --> \n<tr><td><a href=\"http:\/\/alleleseq.gersteinlab.org\/tools.html\" id=\"link-23801\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlleleSeq<\/a>\n<!-- Time to render name section of link id 23801: 2.1457672119141E-6 --> \n<\/td>\n<td><p>pipeline which constructs a diploid personal genome from genomic sequence variants of a family trio, including SNPs, indels and structural variants and maps functional genomic data onto this personal genome.<\/p>\n<!-- Time to render link large description section of link id 23801: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23801: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23801: 0.0001227855682373 --> \n<tr><td><a href=\"http:\/\/jordan.biology.gatech.edu\/page\/software\/broadpeak\/\" id=\"link-24164\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BroadPeak<\/a>\n<!-- Time to render name section of link id 24164: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BroadPeak broad peak calling algorithm for diffuse ChIP-seq datasets.<\/p>\n<!-- Time to render link large description section of link id 24164: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24164: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24164: 0.00017690658569336 --> \n<tr><td><a href=\"http:\/\/deweylab.biostat.wisc.edu\/csem\/\" id=\"link-24188\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">csem<\/a>\n<!-- Time to render name section of link id 24188: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CSEM is a ChIP-Seq multi-read allocator. CSEM stands for ChIP-Seq multi-read allocation using Expectation-Maximization.<\/p>\n<!-- Time to render link large description section of link id 24188: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_csem> How to use <\/a>\n<!-- Time to render notes section of link id 24188: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24188: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/danposdoc\/\" id=\"link-23851\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DANPOS2<\/a>\n<!-- Time to render name section of link id 23851: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2<\/p>\n<!-- Time to render link large description section of link id 23851: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23851: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23851: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/git.embl.de\/grp-zaugg\/diffTF\" id=\"link-25244\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">diffTF<\/a>\n<!-- Time to render name section of link id 25244: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressor.<\/p>\n<!-- Time to render link large description section of link id 25244: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_diffTF> How to use <\/a>\n<!-- Time to render notes section of link id 25244: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25244: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/biocore-ntnu\/epic2\" id=\"link-25726\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">epic2<\/a>\n<!-- Time to render name section of link id 25726: 1.9073486328125E-6 --> \n<\/td>\n<td><p>epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use.<\/p>\n<!-- Time to render link large description section of link id 25726: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_epic2> How to use <\/a>\n<!-- Time to render notes section of link id 25726: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25726: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/groups.csail.mit.edu\/cgs\/gem\/\" id=\"link-25246\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEM<\/a>\n<!-- Time to render name section of link id 25246: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GEM is a scientific software for studying protein-DNA interaction at high resolution using ChIP-seq\/ChIP-exo data. It can also be applied to CLIP-seq and Branch-seq data.<\/p>\n<!-- Time to render link large description section of link id 25246: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEM> How to use <\/a>\n<!-- Time to render notes section of link id 25246: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25246: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/kundajelab\/idr\" id=\"link-24691\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IDR<\/a>\n<!-- Time to render name section of link id 24691: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The IDR (Irreproducible Discovery Rate) framework is a uni\ufb01ed approach to measure the reproducibility of \ufb01ndings identi\ufb01ed from replicate experiments and provide highly stable thresholds based on reproducibility.<\/p>\n<!-- Time to render link large description section of link id 24691: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IDR> How to use <\/a>\n<!-- Time to render notes section of link id 24691: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24691: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/macs3-project\/MACS\" id=\"link-23659\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MACS<\/a>\n<!-- Time to render name section of link id 23659: 2.1457672119141E-6 --> \n<\/td>\n<td><p>We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina \/ Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples.<\/p>\n<!-- Time to render link large description section of link id 23659: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MACS> How to use <\/a>\n<!-- Time to render notes section of link id 23659: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23659: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/asroopra\/MAGIC\" id=\"link-24362\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAGIC<\/a>\n<!-- Time to render name section of link id 24362: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data.<\/p>\n<!-- Time to render link large description section of link id 24362: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24362: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24362: 0.00014400482177734 --> \n<tr><td><a href=\"https:\/\/github.com\/Genometric\/MSPC\/\" id=\"link-25674\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MSPC<\/a>\n<!-- Time to render name section of link id 25674: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Improve Sensitivity and Specificity of Peak Calling, and Identify Consensus Regions<\/p>\n<!-- Time to render link large description section of link id 25674: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MSPC> How to use <\/a>\n<!-- Time to render notes section of link id 25674: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25674: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/genome.gsc.riken.jp\/osc\/english\/dataresource\/\" id=\"link-24402\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MuMRescueLite<\/a>\n<!-- Time to render name section of link id 24402: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MuMRescueLite is the software that enable to use the tag sequencies of mapped to multiple loci to the genome, for the expression analysis. At the mapping of short sequence tags of CAGE or ChIP-Seq to the genome, sequence tags that map to multiple genomic loci (multi-mapping tags or MuMs), are routinely omitted from further analysis, leading to experimental bias and reduced coverage. MuMRescueLite probabilistically reincorporates multi-mapping tags into mapped short read data with acceptable computational requirements.<\/p>\n<!-- Time to render link large description section of link id 24402: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24402: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24402: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/younglab.wi.mit.edu\/super_enhancer_code.html\" id=\"link-24504\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ROSE<\/a>\n<!-- Time to render name section of link id 24504: 1.9073486328125E-6 --> \n<\/td>\n<td><p>To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)<\/p>\n<!-- Time to render link large description section of link id 24504: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ROSE> How to use <\/a>\n<!-- Time to render notes section of link id 24504: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24504: 0.0001068115234375 --> \n<tr><td><a href=\"http:\/\/smithlabresearch.org\/software\/rseg\/\" id=\"link-24505\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RSEG<\/a>\n<!-- Time to render name section of link id 24505: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers.<\/p>\n<!-- Time to render link large description section of link id 24505: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24505: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24505: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/zanglab\/SICER2\" id=\"link-24518\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SICER2<\/a>\n<!-- Time to render name section of link id 24518: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Redesigned and improved version of the original ChIP-seq broad peak calling tool SICER.<\/p>\n<!-- Time to render link large description section of link id 24518: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SICER2> How t o use <\/a>\n<!-- Time to render notes section of link id 24518: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24518: 0.00010800361633301 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n   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class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/pierrepeterlongo\/back_to_sequences\" id=\"link-25269\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Back_to_sequences<\/a>\n<!-- Time to render name section of link id 25269: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Given a set of kmers (fasta \/ fastq <.gz> format) and a set of sequences (fasta \/ fastq <.gz> format), this tool will extract the sequences containing some of those kmers.<\/p>\n<!-- Time to render link large description section of link id 25269: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Back_to_sequences> How to use <\/a>\n<!-- Time to render notes section of link id 25269: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25269: 0.00014185905456543 --> \n<tr><td><a href=\"https:\/\/developer.basespace.illumina.com\/docs\/content\/documentation\/cli\/cli-overview\" id=\"link-26129\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BaseSpace_CLI<\/a>\n<!-- Time to render name section of link id 26129: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Command line interface to work with BaseSpace Sequence Hub data.<\/p>\n<!-- Time to render link large description section of link id 26129: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BaseSpace_CLI> How to use <\/a>\n<!-- Time to render notes section of link id 26129: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26129: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/DominikBuchner\/BOLDigger2\" id=\"link-25523\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BOLDigger2<\/a>\n<!-- Time to render name section of link id 25523: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An even better Python program to query .fasta files against the COI database of www.boldsystems.org<\/p>\n<!-- Time to render link large description section of link id 25523: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BOLDigger2> How to use <\/a>\n<!-- Time to render notes section of link id 25523: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25523: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/rhysf\/DIAMOND2GO\" id=\"link-25540\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIAMOND2GO<\/a>\n<!-- Time to render name section of link id 25540: 2.1457672119141E-6 --> \n<\/td>\n<td>Diamond2GO is a set of tools that can rapidly assign gene ontology and perform enrichment for functional genomics.\n<!-- Time to render link large description section of link id 25540: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Diamond2GO> How to use <\/a>\n<!-- Time to render notes section of link id 25540: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25540: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/NBISweden\/EMBLmyGFF3\" id=\"link-26160\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMBLmyGFF3<\/a>\n<!-- Time to render name section of link id 26160: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An efficient way to convert gff3 annotation files into EMBL format ready to submit.<\/p>\n<!-- Time to render link large description section of link id 26160: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMBLmyGFF3> How to use <\/a>\n<!-- Time to render notes section of link id 26160: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26160: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/enasequence\/enaBrowserTools\" id=\"link-25802\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">enaBrowserTools<\/a>\n<!-- Time to render name section of link id 25802: 2.1457672119141E-6 --> \n<\/td>\n<td><p>enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required.<\/p>\n<!-- Time to render link large description section of link id 25802: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_enaBrowserTools> How to use <\/a>\n<!-- Time to render notes section of link id 25802: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25802: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/pirovc\/ganon\" id=\"link-24855\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ganon<\/a>\n<!-- Time to render name section of link id 24855: 2.8610229492188E-6 --> \n<\/td>\n<td><p>ganon classifies DNA sequences against large sets of genomic reference sequences efficiently.<\/p>\n<!-- Time to render link large description section of link id 24855: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24855: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24855: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/NCI-GDC\/gdc-client\" id=\"link-25622\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gdc-client<\/a>\n<!-- Time to render name section of link id 25622: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The gdc-client provides several convenience functions over the GDC API which provides general download\/upload via HTTPS.<\/p>\n<!-- Time to render link large description section of link id 25622: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gdc-client> How to use <\/a>\n<!-- Time to render notes section of link id 25622: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25622: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/pachterlab\/gget\" id=\"link-24689\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gget<\/a>\n<!-- Time to render name section of link id 24689: 3.0994415283203E-6 --> \n<\/td>\n<td><p>gget enables efficient querying of genomic reference databases.<\/p>\n<!-- Time to render link large description section of link id 24689: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24689: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24689: 0.00011491775512695 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/infernal\/\" id=\"link-23648\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Infernal<\/a>\n<!-- Time to render name section of link id 23648: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).<\/p>\n<!-- Time to render link large description section of link id 23648: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Infernal> How to use <\/a>\n<!-- Time to render notes section of link id 23648: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23648: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/datasets\" id=\"link-25057\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_datasets<\/a>\n<!-- Time to render name section of link id 25057: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. 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id 24775: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24775: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/pauline-ng\/SIFT4G_Annotator\" id=\"link-24724\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SIFT4G_Annotator<\/a>\n<!-- Time to render name section of link id 24724: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Annotating VCF files using the SIFT4G databases.<\/p>\n<!-- Time to render link large description section of link id 24724: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24724: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24724: 0.0001070499420166 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => 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nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1165 level0\"><!-- Div Category --><div id=\"dna-and-protein-language-models\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">DNA and protein language models<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/YU-Zhejian\/art_modern\" id=\"link-26188\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">art_modern<\/a>\n<!-- Time to render name section of link id 26188: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A modern re-implementation of the popular ART simulator with enhanced performance and functionality.<\/p>\n<!-- Time to render link large description section of link id 26188: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_art_modern> How to use <\/a>\n<!-- Time to render notes section of link id 26188: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26188: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Badread\" id=\"link-26191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Badread<\/a>\n<!-- Time to render name section of link id 26191: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Badread is a long-read simulator tool that makes \u2013 you guessed it \u2013 bad reads! It can imitate many kinds of problems one might encounter in real long-read sets: chimeras, low-quality regions, systematic basecalling errors and more.<\/p>\n<!-- Time to render link large description section of link id 26191: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Badread> How to use <\/a>\n<!-- Time to render notes section of link id 26191: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26191: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/niuwa2333\/DTVF\" id=\"link-26173\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DTVF<\/a>\n<!-- Time to render name section of link id 26173: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Virulence Factor Prediction using Deep Learning.<\/p>\n<!-- Time to render link large description section of link id 26173: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DTVF> How to use <\/a>\n<!-- Time to render notes section of link id 26173: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26173: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/google-deepmind\/deepmind-research\/tree\/master\/enformer\" id=\"link-26108\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Enformer<\/a>\n<!-- Time to render name section of link id 26108: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This package provides an implementation of the Enformer model and examples on running the model.<\/p>\n<!-- Time to render link large description section of link id 26108: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Enformer> How to use <\/a>\n<!-- Time to render notes section of link id 26108: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26108: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/facebookresearch\/esm\" id=\"link-26206\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ESM-2<\/a>\n<!-- Time to render name section of link id 26206: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This repository contains code and pre-trained weights for Transformer protein language models from the Meta Fundamental AI Research Protein Team (FAIR), including our state-of-the-art ESM-2 and ESMFold, as well as MSA Transformer, ESM-1v for predicting variant effects and ESM-IF1 for inverse folding<\/p>\n<!-- Time to render link large description section of link id 26206: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ESM-2> How to use <\/a>\n<!-- Time to render notes section of link id 26206: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26206: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/arcinstitute\/evo2\" id=\"link-26113\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Evo2<\/a>\n<!-- Time to render name section of link id 26113: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Evo 2 is a state of the art DNA language model for long context modeling and design.<\/p>\n<!-- Time to render link large description section of link id 26113: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Evo2> How to use <\/a>\n<!-- Time to render notes section of link id 26113: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26113: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/plantcad\/plantcad\" id=\"link-26141\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlantCAD<\/a>\n<!-- Time to render name section of link id 26141: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PlantCaduceus, with its short name of PlantCAD, is a plant DNA LM based on the Caduceus architecture, which extends the efficient Mamba linear-time sequence modeling framework to incorporate bi-directionality and reverse complement equivariance, specifically designed for DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 26141: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlantCAD> How to use <\/a>\n<!-- Time to render notes section of link id 26141: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26141: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/agemagician\/ProtTrans\" id=\"link-26207\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProtTrans<\/a>\n<!-- Time to render name section of link id 26207: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ProtTrans is providing state of the art pretrained language models for proteins.<\/p>\n<!-- Time to render link large description section of link id 26207: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ProtTrans> How to use <\/a>\n<!-- Time to render notes section of link id 26207: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26207: 0.00011491775512695 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1140\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n 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          [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => cgmaptools\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:07:56\n                    [post_modified_gmt] => 2025-05-21 06:07:56\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24870\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 25065\n                    [post_author] => 5\n                    [post_date] => 2023-10-11 09:30:08\n                    [post_date_gmt] => 2023-10-11 07:30:08\n                    [post_content] => <p>[strong]Genobioinfo Cluster: [\/strong] [a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CHEUI] How to use [\/a]<\/p>\n                    [post_title] => CHEUI\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => cheui\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2023-12-05 15:49:04\n                    [post_modified_gmt] => 2023-12-05 14:49:04\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25065\n    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Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00078797340393066-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1140 level0\"><!-- Div Category --><div id=\"epigenetic\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Epigenetic<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/dnaase\/Bis-tools\" id=\"link-24161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BisSNP<\/a>\n<!-- Time to render name section of link id 24161: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Accurate combined SNP\/Methylation calling.<\/p>\n<!-- Time to render link large description section of link id 24161: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24161: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24161: 0.00011920928955078 --> \n<tr><td><a href=\"https:\/\/github.com\/hellbelly\/BS-Snper\" id=\"link-24166\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BS-SNPer<\/a>\n<!-- Time to render name section of link id 24166: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BS-SNPer is an ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM\/SAM format using approximate Bayesian modeling.<\/p>\n<!-- Time to render link large description section of link id 24166: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24166: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24166: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/cgmaptools.github.io\" id=\"link-24870\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cgmaptools<\/a>\n<!-- Time to render name section of link id 24870: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Command-line Toolset for Bisulfite Sequencing Data Analysis.<\/p>\n<!-- Time to render link large description section of link id 24870: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cgmaptools> How to use <\/a>\n<!-- Time to render notes section of link id 24870: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24870: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/comprna\/CHEUI\" id=\"link-25065\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CHEUI<\/a>\n<!-- Time to render name section of link id 25065: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CHEUI (Methylation (CH<sub>3<\/sub>) Estimation Using Ionic current) is an RNA modification detection software for Oxford Nanopore direct RNA sequencing data. CHEUI can be used to detect m6A and m5C in individual reads at single-nucleotide resolution from any sample (e.g. single condition), or detect differential m6A or m5C between any two conditions. CHEUI uses a two-stage deep learning method to detect m6A and m5C transcriptome-wide at single-read and single-site resolution in any sequence context (i.e. without any sequence constrains).<\/p>\n<!-- Time to render link large description section of link id 25065: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CHEUI> How to use <\/a>\n<!-- Time to render notes section of link id 25065: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25065: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfomaticsCSU\/deepsignal\" id=\"link-24197\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepSignal<\/a>\n<!-- Time to render name section of link id 24197: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Detecting methylation using signal-level features from Nanopore sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24197: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24197: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24197: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/al-mcintyre\/mCaller\" id=\"link-24063\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mCaller<\/a>\n<!-- Time to render name section of link id 24063: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This program is designed to call m6A from nanopore data using the differences between measured and expected currents.<\/p>\n<!-- Time to render link large description section of link id 24063: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24063: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24063: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/abardet\/methylasso\" id=\"link-25475\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MethyLasso<\/a>\n<!-- Time to render name section of link id 25475: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole-genome datasets.<\/p>\n<!-- Time to render link large description section of link id 25475: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MethyLasso> How to use <\/a>\n<!-- Time to render notes section of link id 25475: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25475: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/dpryan79\/MethylDackel\" id=\"link-25055\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MethylDackel<\/a>\n<!-- Time to render name section of link id 25055: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MethylDackel (formerly named PileOMeth, which was a temporary name derived due to it using a PILEup to extract METHylation metrics) will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.<\/p>\n<!-- Time to render link large description section of link id 25055: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MethylDackel> How to use <\/a>\n<!-- Time to render notes section of link id 25055: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25055: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/Computomics\/\" id=\"link-24711\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MethylScore<\/a>\n<!-- Time to render name section of link id 24711: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Identification of differentially methylated regions between multiple epigenomes from BS-treated read mappings via methylated region calling.<\/p>\n<!-- Time to render link large description section of link id 24711: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MethylScore> How to use <\/a>\n<!-- Time to render notes section of link id 24711: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24711: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/epi2me-labs\/modbam2bed\" id=\"link-24714\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">modbam2bed<\/a>\n<!-- Time to render name section of link id 24714: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.<\/p>\n<!-- Time to render link large description section of link id 24714: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_modbam2bed> How to use <\/a>\n<!-- Time to render notes section of link id 24714: 1.9073486328125E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24714: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/nf-core\/\" id=\"link-24009\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nf-core workflows<\/a>\n<!-- Time to render name section of link id 24009: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This module provide access to workflows nf-core, there are automatically downloaded into your home.<\/p>\r\n<p><strong>More info at <a href=\"https:\/\/github.com\/nf-core\/configs\/blob\/master\/docs\/genotoul.md\">nf-core\/config<\/a> page.<\/strong><\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 24009: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextflowWorkflows> How to use <\/a>\n<!-- Time to render notes section of link id 24009: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24009: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/bsblabludwig\/rastair\/src\/master\/\" id=\"link-25551\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rastair<\/a>\n<!-- Time to render name section of link id 25551: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast processing of TET-assisted pyridine borane sequencing (TAPS)-based sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25551: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rastair> How to use <\/a>\n<!-- Time to render notes section of link id 25551: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25551: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/guanjue\/S3V2_IDEAS_ESMP\" id=\"link-24507\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">S3V2_IDEAS_ESMP<\/a>\n<!-- Time to render name section of link id 24507: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A package for normalizing, denoising and integrating epigenomic datasets across different cell types.<\/p>\n<!-- Time to render link large description section of link id 24507: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24507: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24507: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/tombo\" id=\"link-24011\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tombo<\/a>\n<!-- Time to render name section of link id 24011: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24011: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- 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class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/arthuryxt\/acfs\" id=\"link-23905\" class=\"track_this_link \" rel=\"noopener noreferrer\">ACFS<\/a>\n<!-- Time to render name section of link id 23905: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Accurate CircRNA Finder Suite. Discovering circRNAs from RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 23905: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23905: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23905: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/tobiasrausch\/alfred\" id=\"link-23978\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Alfred<\/a>\n<!-- Time to render name section of link id 23978: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BAM Statistics, Feature Counting and Annotation<\/p>\n<!-- Time to render link large description section of link id 23978: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23978: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23978: 0.00013017654418945 --> \n<tr><td><a href=\"http:\/\/alleleseq.gersteinlab.org\/tools.html\" id=\"link-23801\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlleleSeq<\/a>\n<!-- Time to render name section of link id 23801: 1.9073486328125E-6 --> \n<\/td>\n<td><p>pipeline which constructs a diploid personal genome from genomic sequence variants of a family trio, including SNPs, indels and structural variants and maps functional genomic data onto this personal genome.<\/p>\n<!-- Time to render link large description section of link id 23801: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23801: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23801: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/suhrig\/arriba\" id=\"link-24143\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Arriba<\/a>\n<!-- Time to render name section of link id 24143: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 24143: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Arriba> How to use <\/a>\n<!-- Time to render notes section of link id 24143: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24143: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/shimlab\/BLAZE\" id=\"link-25811\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BLAZE<\/a>\n<!-- Time to render name section of link id 25811: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Barcode identification from Long reads for AnalyZing single-cell gene Expression. SingleCell Nanopore sequencing data analysis.<\/p>\n<!-- Time to render link large description section of link id 25811: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BLAZE> How to use <\/a>\n<!-- Time to render notes section of link id 25811: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25811: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/pavanvidem\/blockclust\" id=\"link-24025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BlockClust<\/a>\n<!-- Time to render name section of link id 24025: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BlockClust is an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. 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It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.<\/p>\n<!-- Time to render link large description section of link id 24167: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24167: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24167: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/canu\" id=\"link-23781\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">canu<\/a>\n<!-- Time to render name section of link id 23781: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A single molecule sequence assembler for genomes large and small.<\/p>\n<!-- Time to render link large description section of link id 23781: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Canu> How to use <\/a>\n<!-- Time to render notes section of link id 23781: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23781: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/broadinstitute\/CellBender\" id=\"link-24889\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellBender<\/a>\n<!-- Time to render name section of link id 24889: 2.1457672119141E-6 --> \n<\/td>\n<td><p>CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.<\/p>\n<!-- Time to render link large description section of link id 24889: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellBender> How to use <\/a>\n<!-- Time to render notes section of link id 24889: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24889: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell\/software\/pipelines\/latest\/what-is-cell-ranger\" id=\"link-23838\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger<\/a>\n<!-- Time to render name section of link id 23838: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3\u2019 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.<\/p>\n<!-- Time to render link large description section of link id 23838: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRanger> How to use <\/a>\n<!-- Time to render notes section of link id 23838: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23838: 0.00012612342834473 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell-multiome-atac-gex\/software\/overview\/welcome\" id=\"link-24173\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger ARC<\/a>\n<!-- Time to render name section of link id 24173: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Cell Ranger ARC's pipelines analyze sequencing data produced from Chromium Single Cell Multiome ATAC + Gene Expression.<\/p>\n<!-- Time to render link large description section of link id 24173: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRangerARC> How to use <\/a>\n<!-- Time to render notes section of link id 24173: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24173: 0.00012612342834473 --> \n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/chimerascan\" id=\"link-24176\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chimerascan<\/a>\n<!-- Time to render name section of link id 24176: 1.9073486328125E-6 --> \n<\/td>\n<td><p>chimerascan is a software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.<\/p>\n<!-- Time to render link large description section of link id 24176: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24176: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24176: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/Chimera-tools\/ChimPipe\" id=\"link-23891\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ChimPipe<\/a>\n<!-- Time to render name section of link id 23891: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution.<\/p>\n<!-- Time to render link large description section of link id 23891: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23891: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23891: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ChopStitch\" id=\"link-23931\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ChopStitch<\/a>\n<!-- Time to render name section of link id 23931: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23931: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23931: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23931: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/yangence\/circfull\" id=\"link-25401\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">circfull<\/a>\n<!-- Time to render name section of link id 25401: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool to detect and quantify full-length circRNA isoforms from circFL-seq.<\/p>\n<!-- Time to render link large description section of link id 25401: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_circfull> How to use <\/a>\n<!-- Time to render notes section of link id 25401: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25401: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/dieterich-lab\/circtools\" id=\"link-24117\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">circtools<\/a>\n<!-- Time to render name section of link id 24117: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.<\/p>\n<!-- Time to render link large description section of link id 24117: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24117: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24117: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/ciri\" id=\"link-23911\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CIRI<\/a>\n<!-- Time to render name section of link id 23911: 2.1457672119141E-6 --> \n<\/td>\n<td><p>CIRI (circRNA identifier) is a novel chiastic clipping signal based algorithm, which can unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies.<\/p>\n<!-- Time to render link large description section of link id 23911: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23911: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23911: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/MikeAxtell\/CleaveLand4\" id=\"link-24110\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CleaveLand4<\/a>\n<!-- Time to render name section of link id 24110: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Analysis of degradome data to find sliced miRNA and siRNA targets<\/p>\n<!-- Time to render link large description section of link id 24110: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CleaveLand4> How to use <\/a>\n<!-- Time to render notes section of link id 24110: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24110: 0.00012779235839844 --> \n<tr><td><a href=\"https:\/\/www.bio.ifi.lmu.de\/software\/contextmap\/\" id=\"link-24046\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ContextMap2<\/a>\n<!-- Time to render name section of link id 24046: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Fast and accurate context-based RNA-seq mapping. ContextMap determines the most likely origin of a read by evaluating the context of the read in the form of alignments of other reads to the same genomic region. In the original implementation, the focus was on improving initial mappings provided by other mapping tools.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24046: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24046: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24046: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/gitlab.mbb.univ-montp2.fr\/mbb\/CroCo\" id=\"link-23900\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CroCo<\/a>\n<!-- Time to render name section of link id 23900: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification.<\/p>\n<!-- Time to render link large description section of link id 23900: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23900: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23900: 0.00013017654418945 --> \n<tr><td><a href=\"http:\/\/cufflinks.cbcb.umd.edu\" id=\"link-23577\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cufflinks<\/a>\n<!-- Time to render name section of link id 23577: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.<\/p>\n<!-- Time to render link large description section of link id 23577: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cufflink> How to use <\/a>\n<!-- Time to render notes section of link id 23577: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23577: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/devCellPy-Team\/devCellPy\" id=\"link-24805\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">devCellPy<\/a>\n<!-- Time to render name section of link id 24805: 1.9073486328125E-6 --> \n<\/td>\n<td><p>devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing (scRNA-seq).<\/p>\n<!-- Time to render link large description section of link id 24805: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_devCellPy> How to use <\/a>\n<!-- Time to render notes section of link id 24805: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24805: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/git.embl.de\/grp-zaugg\/diffTF\" id=\"link-25244\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">diffTF<\/a>\n<!-- Time to render name section of link id 25244: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressor.<\/p>\n<!-- Time to render link large description section of link id 25244: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_diffTF> How to use <\/a>\n<!-- Time to render notes section of link id 25244: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25244: 0.00010585784912109 --> \n<tr><td><a href=\"http:\/\/www.sigenae.org\/drap\/index.html\" id=\"link-23788\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">drap<\/a>\n<!-- Time to render name section of link id 23788: 1.9073486328125E-6 --> \n<\/td>\n<td><p>De novo RNA-seq Assembly Pipeline<\/p>\n<!-- Time to render link large description section of link id 23788: 0 --> \n<\/td>\n<td>strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DRAP> How to use <\/a>\n<!-- Time to render notes section of link id 23788: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23788: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/google-deepmind\/deepmind-research\/tree\/master\/enformer\" id=\"link-26108\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Enformer<\/a>\n<!-- Time to render name section of link id 26108: 9.5367431640625E-7 --> \n<\/td>\n<td><p>This package provides an implementation of the Enformer model and examples on running the model.<\/p>\n<!-- Time to render link large description section of link id 26108: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Enformer> How to use <\/a>\n<!-- Time to render notes section of link id 26108: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26108: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/erminej.msl.ubc.ca\/\" id=\"link-24215\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ErmineJ<\/a>\n<!-- Time to render name section of link id 24215: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies.<\/p>\n<!-- Time to render link large description section of link id 24215: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24215: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24215: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/mtokuyama\/ERVmap\" id=\"link-24126\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ERVmap<\/a>\n<!-- Time to render name section of link id 24126: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ERVmap is one part curated database of human proviral ERV loci and one part a stringent algorithm to determine which ERVs are transcribed in their RNA seq data.<\/p>\n<!-- Time to render link large description section of link id 24126: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24126: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24126: 0.00013208389282227 --> \n<tr><td><a href=\"https:\/\/pachterlab.github.io\/eXpress\/index.html\" id=\"link-23893\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eXpress<\/a>\n<!-- Time to render name section of link id 23893: 2.1457672119141E-6 --> \n<\/td>\n<td><p>eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.<\/p>\n<!-- Time to render link large description section of link id 23893: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eXpress> How to use <\/a>\n<!-- Time to render notes section of link id 23893: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23893: 0.00012683868408203 --> \n<tr><td><a href=\"https:\/\/github.com\/tderrien\/FEELnc\" id=\"link-23778\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FEELnc<\/a>\n<!-- Time to render name section of link id 23778: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FlExible Extraction of LncRNA.<\/p>\n<!-- Time to render link large description section of link id 23778: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FEELnc> How to use <\/a\n<!-- Time to render notes section of link id 23778: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23778: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/BrooksLabUCSC\/flair\" id=\"link-24236\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAIR<\/a>\n<!-- Time to render name section of link id 24236: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24236: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24236: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24236: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/LuyiTian\/FLAMES\" id=\"link-25920\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAMES<\/a>\n<!-- Time to render name section of link id 25920: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Full-length transcriptome splicing and mutation analysis.<\/p>\n<!-- Time to render link large description section of link id 25920: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FLAMES> How to use <\/a>\n<!-- Time to render notes section of link id 25920: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25920: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/Gaius-Augustus\/GUSHR\" id=\"link-24269\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GUSHR<\/a>\n<!-- Time to render name section of link id 24269: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation. This tool has been adapted to the format needs of AUGUSTUS\/BRAKER and employs GeMoMa for generating UTRs from RNA-Seq coverage data.<\/p>\n<!-- Time to render link large description section of link id 24269: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GUSHR> How to use <\/a>\n<!-- Time to render notes section of link id 24269: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24269: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/RitchieLabIGH\/IRFinder\" id=\"link-24035\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IRFinder<\/a>\n<!-- Time to render name section of link id 24035: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Detecting intron retention from RNA-Seq experiments<\/p>\n<!-- Time to render link large description section of link id 24035: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IRFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24035: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24035: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/alumni.cs.ucr.edu\/~liw\/isolasso.html\" id=\"link-24327\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IsoLasso<\/a>\n<!-- Time to render name section of link id 24327: 2.1457672119141E-6 --> \n<\/td>\n<td><p>IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.<\/p>\n<!-- Time to render link large description section of link id 24327: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24327: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24327: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/pachterlab.github.io\/kallisto\/\" id=\"link-23816\" class=\"track_this_link \" rel=\"noopener noreferrer\">kallisto<\/a>\n<!-- Time to render name section of link id 23816: 2.1457672119141E-6 --> \n<\/td>\n<td><p>kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 23816: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kallisto> How to use <\/a>\n<!-- Time to render notes section of link id 23816: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23816: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/WGLab\/LIQA\" id=\"link-24349\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LIQA<\/a>\n<!-- Time to render name section of link id 24349: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Long-read Isoform Quantification and Analysis) is an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data.<\/p>\n<!-- Time to render link large description section of link id 24349: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24349: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24349: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/mzytnicki\/mmannot\" id=\"link-24395\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mmannot<\/a>\n<!-- Time to render name section of link id 24395: 2.1457672119141E-6 --> \n<\/td>\n<td><p>mmannot annotates reads, or quantifies the features. For instance, suppose that you have sequenced your organism of interest with sRNA-Seq (RNA-Seq works too), and you want to know how many times you have sequenced miRNAs, rRNAs, tRNAs, etc. This is what mmannot does. A huge proportion of the reads may actually map at several locations. These multi-mapping reads are usually handled poorly by similar quantification tools. In our methods, when a read maps at several locations, all these locations are inspected: If all these locations belong to the same feature (e.g. miRNAs, in case of a duplicated gene family), the read is still annotated as a miRNA. If the location belong to different features (e.g. 3'UTR and miRNA), the read is ambiguous, and is flagged as 3'UTR--miRNA. In case 1, we say when have\u00a0rescued\u00a0a read.<\/p>\n<!-- Time to render link large description section of link id 24395: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24395: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24395: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/mzytnicki\/multi-mapping-counter\/overview\" id=\"link-23965\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mmquant<\/a>\n<!-- Time to render name section of link id 23965: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This tool counts the number of reads (produced by RNA-Seq) per gene, much like HTSeq-count and featureCounts. The main difference with other tools is that multi-mapping reads are counted differently: if a read is mapped to gene A, gene B, and gene C, the tool will create a new feature, \"geneA--geneB--geneC\", that will be counted once.<\/p>\n<!-- Time to render link large description section of link id 23965: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mmquant> How to use <\/a>\n<!-- Time to render notes section of link id 23965: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23965: 0.00010776519775391 --> \n<tr><td><a href=\"http:\/\/genome.gsc.riken.jp\/osc\/english\/dataresource\/\" id=\"link-24402\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MuMRescueLite<\/a>\n<!-- Time to render name section of link id 24402: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MuMRescueLite is the software that enable to use the tag sequencies of mapped to multiple loci to the genome, for the expression analysis. At the mapping of short sequence tags of CAGE or ChIP-Seq to the genome, sequence tags that map to multiple genomic loci (multi-mapping tags or MuMs), are routinely omitted from further analysis, leading to experimental bias and reduced coverage. MuMRescueLite probabilistically reincorporates multi-mapping tags into mapped short read data with acceptable computational requirements.<\/p>\n<!-- Time to render link large description section of link id 24402: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24402: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24402: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/a-slide\/NanoCount\" id=\"link-24408\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCount<\/a>\n<!-- Time to render name section of link id 24408: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NanoCount estimates transcripts abundance from Oxford Nanopore direct-RNA sequencing datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads.<\/p>\n<!-- Time to render link large description section of link id 24408: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24408: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24408: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/nf-core\/\" id=\"link-24009\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nf-core workflows<\/a>\n<!-- Time to render name section of link id 24009: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This module provide access to workflows nf-core, there are automatically downloaded into your home.<\/p>\r\n<p><strong>More info at <a href=\"https:\/\/github.com\/nf-core\/configs\/blob\/master\/docs\/genotoul.md\">nf-core\/config<\/a> page.<\/strong><\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 24009: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextflowWorkflows> How to use <\/a>\n<!-- Time to render notes section of link id 24009: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24009: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/pmelsted\/pizzly\" id=\"link-24450\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pizzly<\/a>\n<!-- Time to render name section of link id 24450: 5.0067901611328E-6 --> \n<\/td>\n<td><p>A program for detecting gene fusions from RNA-Seq data of cancer samples.<\/p>\n<!-- Time to render link large description section of link id 24450: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24450: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24450: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/portcullis.readthedocs.io\/en\/latest\/\" id=\"link-23986\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Portcullis<\/a>\n<!-- Time to render name section of link id 23986: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Splice junction analysis and filtering from BAM files.<\/p>\n<!-- Time to render link large description section of link id 23986: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23986: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23986: 0.00011706352233887 --> \n<tr><td><a href=\"http:\/\/deweylab.biostat.wisc.edu\/psginfer\/\" id=\"link-24466\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PSGInfer<\/a>\n<!-- Time to render name section of link id 24466: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PSGInfer is a software package for the analysis of RNA-Seq data with probabilistic splice graph (PSG) models of gene alternative processing (splicing, transcription initiation, and polyadenylation)<\/p>\n<!-- Time to render link large description section of link id 24466: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24466: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24466: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/wososa\/PSI-Sigma\" id=\"link-24467\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PSI-Sigma<\/a>\n<!-- Time to render name section of link id 24467: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. However, previous PSI-detection methods are limited to specific types of AS events. PSI-Sigma is using a new splicing index (PSI\u03a3) that is more flexible, can incoporate novel junctions, and can compute PSI values of individual exons in complex splicing events.<\/p>\n<!-- Time to render link large description section of link id 24467: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24467: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24467: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/dimitris-karapliafis\/RdRpCATCH\" id=\"link-25763\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RdRpCATCH<\/a>\n<!-- Time to render name section of link id 25763: 2.1457672119141E-6 --> \n<\/td>\n<td>A community effort to create a shared resource for HMM-based RdRp discovery \n<!-- Time to render link large description section of link id 25763: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RdRpCATCH> How to use <\/a>\n<!-- Time to render notes section of link id 25763: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25763: 0.00012898445129395 --> \n<tr><td><a href=\"http:\/\/srv00.recas.ba.infn.it\/reditools\/\" id=\"link-23975\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REDItools<\/a>\n<!-- Time to render name section of link id 23975: 1.9073486328125E-6 --> \n<\/td>\n<td><p>REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23975: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23975: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23975: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/kamimrcht\/REINDEER\" id=\"link-24488\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REINDEER<\/a>\n<!-- Time to render name section of link id 24488: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Efficient indexing of k-mer presence and abundance in sequencing datasets.<\/p>\n<!-- Time to render link large description section of link id 24488: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REINDEER> How to use <\/a>\n<!-- Time to render notes section of link id 24488: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24488: 0.0001981258392334 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/rnaseq-mats\/\" id=\"link-23981\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rMATS<\/a>\n<!-- Time to render name section of link id 23981: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns.<\/p>\n<!-- Time to render link large description section of link id 23981: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23981: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23981: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/Xinglab\/rmats-turbo\" id=\"link-24498\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rMATS turbo<\/a>\n<!-- Time to render name section of link id 24498: 2.8610229492188E-6 --> \n<\/td>\n<td><p>rMATS turbo is the C\/Cython version of rMATS (refer to http:\/\/rnaseq-mats.sourceforge.net) : Multivariate Analysis of Transcript Splicing (MATS). The major difference between rMATS turbo and rMATS is speed and space usage.<\/p>\n<!-- Time to render link large description section of link id 24498: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rMATS_turbo> How to use <\/a>\n<!-- Time to render notes section of link id 24498: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24498: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/deweylab.github.io\/RSEM\/\" id=\"link-23877\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RSEM<\/a>\n<!-- Time to render name section of link id 23877: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RSEM (RNA-Seq by Expectation-Maximization) is a software package for estimating gene and isoform expression levels from RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 23877: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RSEM> How to use <\/a>\n<!-- Time to render notes section of link id 23877: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23877: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/rseqc.sourceforge.net\/\" id=\"link-23720\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RSeQC<\/a>\n<!-- Time to render name section of link id 23720: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data<\/p>\n<!-- Time to render link large description section of link id 23720: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RSeQC> How to use <\/a>\n<!-- Time to render notes section of link id 23720: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23720: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/salmon\" id=\"link-23776\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Salmon<\/a>\n<!-- Time to render name section of link id 23776: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Highly-accurate &amp; wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments<\/p>\n<!-- Time to render link large description section of link id 23776: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Salmon> How to use <\/a>\n<!-- Time to render notes section of link id 23776: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23776: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/atarashansky\/SAMap\" id=\"link-25484\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SAMap<\/a>\n<!-- Time to render name section of link id 25484: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.<\/p>\n<!-- Time to render link large description section of link id 25484: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SAMap> How to use <\/a>\n<!-- Time to render notes section of link id 25484: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25484: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/PF2-pasteur-fr\/SARTools\" id=\"link-23722\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SARTools<\/a>\n<!-- Time to render name section of link id 23722: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files.<\/p>\n<!-- Time to render link large description section of link id 23722: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in R-4.5.0\n<!-- Time to render notes section of link id 23722: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23722: 0.00012707710266113 --> \n<tr><td><a href=\"http:\/\/pachterlab.github.io\/sleuth\/\" id=\"link-23777\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sleuth<\/a>\n<!-- Time to render name section of link id 23777: 1.9073486328125E-6 --> \n<\/td>\n<td><p>sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.<\/p>\n<!-- Time to render link large description section of link id 23777: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23777: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23777: 0.0001220703125 --> \n<tr><td><a href=\"https:\/\/github.com\/aquaskyline\/SOAPdenovo-Trans\" id=\"link-24527\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SOAPdenovo-Trans<\/a>\n<!-- Time to render name section of link id 24527: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.<\/p>\n<!-- Time to render link large description section of link id 24527: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24527: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24527: 0.00011920928955078 --> \n<tr><td><a href=\"http:\/\/bioinfo.lifl.fr\/RNA\/sortmerna\/index.php\" id=\"link-23734\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SortMeRNA<\/a>\n<!-- Time to render name section of link id 23734: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity<\/p>\n<!-- Time to render link large description section of link id 23734: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SortMeRNA> How to use <\/a>\n<!-- Time to render notes section of link id 23734: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23734: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/wheaton5\/souporcell\" id=\"link-25263\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">souporcell<\/a>\n<!-- Time to render name section of link id 25263: 2.1457672119141E-6 --> \n<\/td>\n<td><p>souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.<\/p>\n<!-- Time to render link large description section of link id 25263: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_souporcell> How to use <\/a>\n<!-- Time to render notes section of link id 25263: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25263: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/spatial-gene-expression\/software\/pipelines\/latest\/what-is-space-ranger\" id=\"link-24530\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpaceRanger<\/a>\n<!-- Time to render name section of link id 24530: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield and fluorescence microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.<\/p>\n<!-- Time to render link large description section of link id 24530: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SpaceRanger> How to use <\/a>\n<!-- Time to render notes section of link id 24530: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24530: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/splicegrapher\/\" id=\"link-24533\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpliceGrapher<\/a>\n<!-- Time to render name section of link id 24533: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SpliceGrapher predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene's exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.<\/p>\n<!-- Time to render link large description section of link id 24533: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24533: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24533: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/flemingtonlab\/SpliceTools\" id=\"link-25326\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpliceTools<\/a>\n<!-- Time to render name section of link id 25326: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing, Nucleic Acids Research, 2023.<\/p>\n<!-- Time to render link large description section of link id 25326: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SpliceTools> How to use <\/a>\n<!-- Time to render notes section of link id 25326: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25326: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/ConesaLab\/SQANTI3\" id=\"link-24537\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SQANTI3<\/a>\n<!-- Time to render name section of link id 24537: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SQANTI3 is the newest version of the SQANTI tool (publication) that merges features from SQANTI, (code repository) and SQANTI2 (code repository), together with new additions. SQANTI3 will continue as an integrated development aiming to providing you the best characterization possible for your new long read-defined transcriptome. SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, that also includes IsoAnnot and tappAS.<\/p>\n<!-- Time to render link large description section of link id 24537: 8.1062316894531E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24537: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24537: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/wyang17\/SQuIRE\" id=\"link-24539\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SQuIRE<\/a>\n<!-- Time to render name section of link id 24539: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SQuIRE reveals locus-specific regulation of interspersed repeat expression, Nucleic Acids Research<\/p>\n<!-- Time to render link large description section of link id 24539: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SQuIRE> How to use <\/a>\n<!-- Time to render notes section of link id 24539: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24539: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/alexdobin\/STAR\" id=\"link-23912\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STAR<\/a>\n<!-- Time to render name section of link id 23912: 2.1457672119141E-6 --> \n<\/td>\n<td><p><span class=\"col-11 text-gray-dark mr-2\">RNA-seq aligner<\/span><\/p>\n<!-- Time to render link large description section of link id 23912: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_STAR> How to use <\/a>\n<!-- Time to render notes section of link id 23912: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23912: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/STAR-Fusion\/STAR-Fusion\" id=\"link-23740\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STAR-Fusion<\/a>\n<!-- Time to render name section of link id 23740: 1.9073486328125E-6 --> \n<\/td>\n<td><p>STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set (using a GTF file, ideally the same annotation file used during the STAR genome index building process during the intial STAR setup).<\/p>\n<!-- Time to render link large description section of link id 23740: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_STAR-Fusion> How to use <\/a>\n<!-- Time to render notes section of link id 23740: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23740: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/stringtie\" id=\"link-23741\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">StringTie<\/a>\n<!-- Time to render name section of link id 23741: 1.9073486328125E-6 --> \n<\/td>\n<td><p><b>StringTie<\/b> is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional <i>de novo<\/i> assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.<\/p>\n<!-- Time to render link large description section of link id 23741: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_StringTie> How to use <\/a>\n<!-- Time to render notes section of link id 23741: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23741: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/bioinf.wehi.edu.au\/subread-package\/\" id=\"link-23743\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Subread<\/a>\n<!-- Time to render name section of link id 23743: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool kit for processing next-gen sequencing data<\/p>\n<!-- Time to render link large description section of link id 23743: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Subread> How to use <\/a>\n<!-- Time to render notes section of link id 23743: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23743: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/comprna\/SUPPA\" id=\"link-23970\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SUPPA<\/a>\n<!-- Time to render name section of link id 23970: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.<\/p>\n<!-- Time to render link large description section of link id 23970: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SUPPA> How to use <\/a>\n<!-- Time to render notes section of link id 23970: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23970: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/tacorna\/taco\" id=\"link-25534\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TACO<\/a>\n<!-- Time to render name section of link id 25534: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Multi-sample transcriptome assembly from RNA-Seq.<\/p>\n<!-- Time to render link large description section of link id 25534: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TACO> How to use <\/a>\n<!-- Time to render notes section of link id 25534: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25534: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/GenomeRIK\/tama\" id=\"link-24557\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TAMA<\/a>\n<!-- Time to render name section of link id 24557: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Transcriptome Annotation by Modular Algorithms: this software was designed for processing Iso-Seq data and other long read transcriptome data.<\/p>\n<!-- Time to render link large description section of link id 24557: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TAMA> How to use <\/a>\n<!-- Time to render notes section of link id 24557: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24557: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/arefeen\/TAPAS\" id=\"link-25322\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TAPAS<\/a>\n<!-- Time to render name section of link id 25322: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tool for Alternative Polyadenylation Site Analysis.<\/p>\n<!-- Time to render link large description section of link id 25322: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TAPAS> How to use <\/a>\n<!-- Time to render notes section of link id 25322: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25322: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/TPMCalculator\" id=\"link-24071\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TPMCalculator<\/a>\n<!-- Time to render name section of link id 24071: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.<\/p>\n<!-- Time to render link large description section of link id 24071: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TPMCalculator> How to use <\/a>\n<!-- Time to render notes section of link id 24071: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24071: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/hibberdlab.com\/transrate\/index.html\" id=\"link-23775\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Transrate<\/a>\n<!-- Time to render name section of link id 23775: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Transrate is software for de-novo transcriptome assembly quality analysis.<\/p>\n<!-- Time to render link large description section of link id 23775: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Transrate> How to use <\/a>\n<!-- Time to render notes section of link id 23775: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23775: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/trinotate.sourceforge.net\/\" id=\"link-23756\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trinotate<\/a>\n<!-- Time to render name section of link id 23756: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.<\/p>\n<!-- Time to render link large description section of link id 23756: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23756: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23756: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/timbitz\/Whippet.jl\" id=\"link-24593\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Whippet<\/a>\n<!-- Time to render name section of link id 24593: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Lightweight and Fast RNA-seq quantification at the event-level<\/p>\n<!-- Time to render link large description section of link id 24593: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24593: 0 --> 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[0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00073981285095215-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1148 level0\"><!-- Div Category --><div id=\"gene-fusion\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Gene fusion<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/chimerascan\" id=\"link-24176\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chimerascan<\/a>\n<!-- Time to render name section of link id 24176: 1.9073486328125E-6 --> \n<\/td>\n<td><p>chimerascan is a software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.<\/p>\n<!-- Time to render link large description section of link id 24176: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24176: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24176: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/pmelsted\/pizzly\" id=\"link-24450\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pizzly<\/a>\n<!-- Time to render name section of link id 24450: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A program for detecting gene fusions from RNA-Seq data of cancer samples.<\/p>\n<!-- Time to render link large description section of link id 24450: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24450: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24450: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/STAR-Fusion\/STAR-Fusion\" id=\"link-23740\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STAR-Fusion<\/a>\n<!-- Time to render name section of link id 23740: 2.1457672119141E-6 --> \n<\/td>\n<td><p>STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set (using a GTF file, ideally the same annotation file used during the STAR genome index building process during the intial STAR setup).<\/p>\n<!-- Time to render link large description section of link id 23740: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_STAR-Fusion> How to use <\/a>\n<!-- Time to render notes section of link id 23740: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23740: 0.00011897087097168 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1123\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    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wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1123)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 23604\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:30\n                    [post_date_gmt] => 2022-11-22 09:25:30\n                    [post_content] => \n                    [post_title] => Carthagene\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => carthagene\n                    [to_ping] => \n                    [pinged] => \n                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raw\n                )\n\n        )\n\n    [post_count] => 3\n    [current_post] => -1\n    [in_the_loop] => \n    [post] => WP_Post Object\n        (\n            [ID] => 23604\n            [post_author] => 5\n            [post_date] => 2022-11-22 10:25:30\n            [post_date_gmt] => 2022-11-22 09:25:30\n            [post_content] => \n            [post_title] => Carthagene\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => carthagene\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2025-05-21 07:54:03\n            [post_modified_gmt] => 2025-05-21 05:54:03\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/carthagene\/\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 3\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    [is_category] => \n    [is_tag] => \n    [is_tax] => 1\n    [is_search] => \n    [is_feed] => \n    [is_comment_feed] => \n    [is_trackback] => \n    [is_home] => \n    [is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => 77de6bf0aad7a8279e46cde42b13c3dd\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00066781044006348-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1123 level0\"><!-- Div Category --><div id=\"genetic-map\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Genetic map<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"http:\/\/www.inra.fr\/mia\/T\/CarthaGene\/\" id=\"link-23604\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Carthagene<\/a>\n<!-- Time to render name section of link id 23604: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CarthaGene is a genetic\/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. CarthaGene can handle data made up of several distinct populations which t may each be either F2 backcross, recombinant inbred lines, F2 t intercross, phase known outbreds and\/or radiated hybrids (haploid t and diploid data).<\/p>\n<!-- Time to render link large description section of link id 23604: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23604: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23604: 0.00013208389282227 --> \n<tr><td><a href=\"http:\/\/catchenlab.life.illinois.edu\/chromonomer\/\" id=\"link-24178\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Chromonomer<\/a>\n<!-- Time to render name section of link id 24178: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Chromonomer is a program designed to integrate a genome assembly with a genetic map.<\/p>\n<!-- Time to render link large description section of link id 24178: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24178: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24178: 0.00012993812561035 --> \n<tr><td><a href=\"https:\/\/github.com\/TF-Chan-Lab\/OMBlast\" id=\"link-24004\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OMBlast<\/a>\n<!-- Time to render name section of link id 24004: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An alignment tool for optical mapping data.<\/p>\n<!-- Time to render link large description section of link id 24004: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24004: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24004: 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(\n                    [ID] => 24750\n                    [post_author] => 5\n                    [post_date] => 2023-03-02 14:15:00\n                    [post_date_gmt] => 2023-03-02 13:15:00\n                    [post_content] => \n                    [post_title] => ASMC\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => asmc\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-02-09 07:57:36\n                    [post_modified_gmt] => 2026-02-09 06:57:36\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24750\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 24745\n                    [post_author] => 5\n                    [post_date] => 2023-02-28 08:09:43\n                    [post_date_gmt] => 2023-02-28 07:09:43\n                    [post_content] => \n                    [post_title] => BAMscorer\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bamscorer\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:33:10\n                    [post_modified_gmt] => 2025-05-21 05:33:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24745\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 24987\n                    [post_author] => 5\n                    [post_date] => 2023-07-19 12:48:14\n                    [post_date_gmt] => 2023-07-19 10:48:14\n                    [post_content] => \n                    [post_title] => Beagle_Utilities\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => beagle_utilities\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:35:58\n                    [post_modified_gmt] => 2025-05-21 05:35:58\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24987\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 25588\n                    [post_author] => 5\n                    [post_date] => 2024-11-27 07:08:39\n                    [post_date_gmt] => 2024-11-27 06:08:39\n                    [post_content] => \n                    [post_title] => BeXY\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bexy\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-12-18 09:43:51\n                    [post_modified_gmt] => 2024-12-18 08:43:51\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25588\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [4] => WP_Post Object\n                (\n                    [ID] => 24840\n                    [post_author] => 1\n                    [post_date] => 2023-05-03 10:07:32\n                    [post_date_gmt] => 2023-05-03 08:07:32\n                    [post_content] => \n                    [post_title] => demuxlet\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => demuxlet\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 13:56:23\n                    [post_modified_gmt] => 2025-05-21 11:56:23\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24840\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [5] => WP_Post Object\n                (\n                    [ID] => 25060\n                    [post_author] => 5\n                    [post_date] => 2023-10-04 09:20:42\n                    [post_date_gmt] => 2023-10-04 07:20:42\n                    [post_content] => \n                    [post_title] => EMMAX\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => emmax\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2023-12-05 16:07:55\n                    [post_modified_gmt] => 2023-12-05 15:07:55\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25060\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [6] => WP_Post Object\n                (\n                    [ID] => 25466\n                    [post_author] => 5\n                    [post_date] => 2024-06-24 16:01:48\n                    [post_date_gmt] => 2024-06-24 14:01:48\n                    [post_content] => \n                    [post_title] => evalAdmix\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => evaladmix\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-07-11 09:28:45\n                    [post_modified_gmt] => 2024-07-11 07:28:45\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25466\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [7] => WP_Post Object\n                (\n                    [ID] => 25491\n                    [post_author] => 5\n                    [post_date] => 2024-07-15 14:11:19\n                    [post_date_gmt] => 2024-07-15 12:11:19\n                    [post_content] => \n                    [post_title] => gamevar.f90\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => gamevar-f90\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-08-12 08:11:01\n                    [post_modified_gmt] => 2024-08-12 06:11:01\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25491\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [8] => WP_Post Object\n                (\n                    [ID] => 25650\n                    [post_author] => 5\n                    [post_date] => 2025-01-27 12:50:18\n                    [post_date_gmt] => 2025-01-27 11:50:18\n                    [post_content] => \n                    [post_title] => GARLIC\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => garlic\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-03-02 20:12:46\n                    [post_modified_gmt] => 2025-03-02 19:12:46\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25650\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [9] => WP_Post Object\n                (\n                    [ID] => 25444\n                    [post_author] => 5\n                    [post_date] => 2024-06-11 10:21:56\n                    [post_date_gmt] => 2024-06-11 08:21:56\n                    [post_content] => \n                    [post_title] => GONE\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => gone\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-19 09:47:53\n                    [post_modified_gmt] => 2024-06-19 07:47:53\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25444\n                    [menu_order] => 0\n      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[post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25149\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 25804\n                    [post_author] => 5\n                    [post_date] => 2025-05-15 13:10:01\n                    [post_date_gmt] => 2025-05-15 11:10:01\n                    [post_content] => \n                    [post_title] => loco-pipe\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => loco-pipe\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-06-25 11:38:20\n                    [post_modified_gmt] => 2025-06-25 09:38:20\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25804\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [12] => WP_Post Object\n                (\n                    [ID] => 25359\n                    [post_author] => 5\n                    [post_date] => 2024-04-25 14:00:18\n                    [post_date_gmt] => 2024-04-25 12:00:18\n                    [post_content] => \n                    [post_title] => moments\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => moments\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-19 10:12:22\n                    [post_modified_gmt] => 2024-06-19 08:12:22\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25359\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [13] => WP_Post Object\n                (\n                    [ID] => 25731\n                    [post_author] => 5\n                    [post_date] => 2025-03-20 07:46:01\n                    [post_date_gmt] => 2025-03-20 06:46:01\n                    [post_content] => \n                    [post_title] => PopART\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => popart\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-06-25 11:13:27\n                    [post_modified_gmt] => 2025-06-25 09:13:27\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25731\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    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https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25272\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [15] => WP_Post Object\n                (\n                    [ID] => 25589\n                    [post_author] => 5\n                    [post_date] => 2024-12-02 14:40:53\n                    [post_date_gmt] => 2024-12-02 13:40:53\n                    [post_content] => \n                    [post_title] => POPS\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => pops\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-12-18 10:02:26\n                    [post_modified_gmt] => 2024-12-18 09:02:26\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25589\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [16] => WP_Post Object\n                (\n                    [ID] => 25294\n                    [post_author] => 5\n                    [post_date] => 2024-03-11 14:40:49\n                    [post_date_gmt] => 2024-03-11 13:40:49\n                    [post_content] => \n                    [post_title] => pyrho\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => pyrho\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-12 10:58:53\n                    [post_modified_gmt] => 2024-03-12 09:58:53\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25294\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [17] => WP_Post Object\n                (\n                    [ID] => 25289\n                    [post_author] => 5\n                    [post_date] => 2024-03-11 09:19:01\n                    [post_date_gmt] => 2024-03-11 08:19:01\n                    [post_content] => <p>quickLD (qLD) is a tool to calculate Linkage disequilibrium (the non-random association between alleles at different loci).<\/p>\n                    [post_title] => quickLD\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => quickld\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-12 11:02:24\n                    [post_modified_gmt] => 2024-03-12 10:02:24\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25289\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n      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[post_date_gmt] => 2023-03-02 13:15:00\n            [post_content] => \n            [post_title] => ASMC\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => asmc\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2026-02-09 07:57:36\n            [post_modified_gmt] => 2026-02-09 06:57:36\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24750\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 21\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    [is_category] => \n    [is_tag] => \n    [is_tax] => 1\n    [is_search] => \n    [is_feed] => \n    [is_comment_feed] => \n    [is_trackback] => \n    [is_home] => \n    [is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => de9f3807666d584d33208fbc76690ab2\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00085902214050293-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1159 level0\"><!-- Div Category --><div id=\"genetics\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Genetics<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/PalamaraLab\/ASMC\" id=\"link-24750\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASMC<\/a>\n<!-- Time to render name section of link id 24750: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ascertained Sequentially Markovian Coalescent (contains ASMC and an extension, FastSMC, together with python bindings for both)<\/p>\n<!-- Time to render link large description section of link id 24750: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ASMC> How to use <\/a>\n<!-- Time to render notes section of link id 24750: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24750: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/laneatmore\/BAMscorer\" id=\"link-24745\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BAMscorer<\/a>\n<!-- Time to render name section of link id 24745: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BAMscorer can be used to conduct genomic assignment tests from BAM files. Assignments can be done on genomic regions, inversions, and whole-genome datasets.<\/p>\n<!-- Time to render link large description section of link id 24745: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24745: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24745: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/faculty.washington.edu\/browning\/beagle_utilities\/utilities.html\" id=\"link-24987\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle_Utilities<\/a>\n<!-- Time to render name section of link id 24987: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Simple utility programs for manipulating text files, especially VCF files.<\/p>\n<!-- Time to render link large description section of link id 24987: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24987: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24987: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/wegmannlab\/bexy\/src\/master\/\" id=\"link-25588\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BeXY<\/a>\n<!-- Time to render name section of link id 25588: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BeXY is a tool to jointly infer sex karyotypes and sex-linked scaffolds from read count data. It can also be used to genetically sex single individuals. BeXY is a command-line tool, and we provide an easy-to-use R package to visualize and parse the results.<\/p>\n<!-- Time to render link large description section of link id 25588: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BeXY> How to use <\/a>\n<!-- Time to render notes section of link id 25588: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25588: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/statgen\/demuxlet\" id=\"link-24840\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">demuxlet<\/a>\n<!-- Time to render name section of link id 24840: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Genetic multiplexing of barcoded single cell RNA-seq<\/p>\n<!-- Time to render link large description section of link id 24840: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_demuxlet> How to use <\/a>\n<!-- Time to render notes section of link id 24840: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24840: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/genome.sph.umich.edu\/wiki\/EMMAX\" id=\"link-25060\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMMAX<\/a>\n<!-- Time to render name section of link id 25060: 3.0994415283203E-6 --> \n<\/td>\n<td><p><b>EMMAX<\/b>\u00a0is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.<\/p>\n<!-- Time to render link large description section of link id 25060: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMMAX> How to use <\/a>\n<!-- Time to render notes section of link id 25060: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25060: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/GenisGE\/evalAdmix\" id=\"link-25466\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">evalAdmix<\/a>\n<!-- Time to render name section of link id 25466: 1.9073486328125E-6 --> \n<\/td>\n<td><p>evalAdmix allows to evaluate the results of an admixture analysis (i.e. the result of applying ADMIXTURE, STRUCTURE, NGSadmix and similar).<\/p>\n<!-- Time to render link large description section of link id 25466: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_evalAdmix> How to use <\/a>\n<!-- Time to render notes section of link id 25466: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25466: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/djordand2008\/gamevar.f90\" id=\"link-25491\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gamevar.f90<\/a>\n<!-- Time to render name section of link id 25491: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A software package for calculating individual genetic diversity.<\/p>\n<!-- Time to render link large description section of link id 25491: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gamevar.f90> How to use <\/a>\n<!-- Time to render notes section of link id 25491: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25491: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/github.com\/szpiech\/garlic\" id=\"link-25650\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GARLIC<\/a>\n<!-- Time to render name section of link id 25650: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GARLIC is a program for calling runs of homozygosity in genotype data. It implements the ROH calling method of Pemberton et al. AJHG (2012) and Blant et al. (2017)<\/p>\n<!-- Time to render link large description section of link id 25650: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GARLIC> How to use <\/a>\n<!-- Time to render notes section of link id 25650: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25650: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/github.com\/esrud\/GONE\" id=\"link-25444\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GONE<\/a>\n<!-- Time to render name section of link id 25444: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This program calculates and uses linkage disequilibrium at genomic marker loci to infer the effective population size trajectories over a period of about 100-200 hundred generations back in time.<\/p>\n<!-- Time to render link large description section of link id 25444: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GONE> How to use <\/a>\n<!-- Time to render notes section of link id 25444: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25444: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/browning-lab\/hap-ibd\" id=\"link-25149\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hap-ibd<\/a>\n<!-- Time to render name section of link id 25149: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.<\/p>\n<!-- Time to render link large description section of link id 25149: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hap-ibd> How to use <\/a>\n<!-- Time to render notes section of link id 25149: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25149: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/sudmantlab\/loco-pipe\" id=\"link-25804\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">loco-pipe<\/a>\n<!-- Time to render name section of link id 25804: 2.1457672119141E-6 --> \n<\/td>\n<td><p>loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data.<\/p>\n<!-- Time to render link large description section of link id 25804: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_loco-pipe> How to use <\/a>\n<!-- Time to render notes section of link id 25804: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25804: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/moments.readthedocs.io\/en\/main\/index.html\" id=\"link-25359\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">moments<\/a>\n<!-- Time to render name section of link id 25359: 2.1457672119141E-6 --> \n<\/td>\n<td><p>moments implements methods for inferring demographic history and patterns of selection from genetic data, based on solutions to the diffusion approximations to the site-frequency spectrum (SFS).<\/p>\n<!-- Time to render link large description section of link id 25359: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_moments> How to use <\/a>\n<!-- Time to render notes section of link id 25359: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25359: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/popart.maths.otago.ac.nz\/\" id=\"link-25731\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PopART<\/a>\n<!-- Time to render name section of link id 25731: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PopART (Population Analysis with Reticulate Trees) is free, open source population genetics software that was developed as part of the Allan Wilson Centre Imaging Evolution Initiative.<\/p>\n<!-- Time to render link large description section of link id 25731: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PopART> How to use <\/a>\n<!-- Time to render notes section of link id 25731: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25731: 0.0001220703125 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/popoolation\/?source=navbar\" id=\"link-25272\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PoPoolation<\/a>\n<!-- Time to render name section of link id 25272: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima\u2019s Pi, Watterson\u2019s Theta and Tajima\u2019s D with a sliding window approach for chromosomes or for set of genes.<\/p>\n<!-- Time to render link large description section of link id 25272: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PoPoolation> How to use <\/a>\n<!-- Time to render notes section of link id 25272: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25272: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/membres-timc.imag.fr\/Olivier.Francois\/pops.html\" id=\"link-25589\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">POPS<\/a>\n<!-- Time to render name section of link id 25589: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The POPS program performs inference of ancestry distribution models.<\/p>\n<!-- Time to render link large description section of link id 25589: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_POPS> How to use <\/a>\n<!-- Time to render notes section of link id 25589: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25589: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenmethods\/pyrho\" id=\"link-25294\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pyrho<\/a>\n<!-- Time to render name section of link id 25294: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast demography-aware inference of fine-scale recombination rates based on fused-LASSO.<\/p>\n<!-- Time to render link large description section of link id 25294: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pyrho> How to use <\/a>\n<!-- Time to render notes section of link id 25294: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25294: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/pephco\/quickLD\" id=\"link-25289\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quickLD<\/a>\n<!-- Time to render name section of link id 25289: 2.1457672119141E-6 --> \n<\/td>\n<td><p>High-performance Computation of Linkage Disequilibrium on CPUs and GPUs.<\/p>\n<!-- Time to render link large description section of link id 25289: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_quickLD> How to use <\/a>\n<!-- Time to render notes section of link id 25289: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25289: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/GuntherLab\/READv2\" id=\"link-25546\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">READv2<\/a>\n<!-- Time to render name section of link id 25546: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Relationship Estimation from Ancient DNA version 2.<\/p>\n<!-- Time to render link large description section of link id 25546: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_READv2> How to use <\/a>\n<!-- Time to render notes section of link id 25546: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25546: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/simon.boitard\/snt\/\" id=\"link-25665\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SelNeTime<\/a>\n<!-- Time to render name section of link id 25665: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The selnetime python package implements methods for statistical analysis of genetic data collected for a same population at different times.<\/p>\n<!-- Time to render link large description section of link id 25665: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SelNeTime> How to use <\/a>\n<!-- Time to render notes section of link id 25665: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25665: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/atks\/vt\" id=\"link-25487\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vt<\/a>\n<!-- Time to render name section of link id 25487: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool set for short variant discovery in genetic sequence data.<\/p>\n<!-- Time to render link large description section of link id 25487: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vt> How to use <\/a>\n<!-- Time to render notes section of link id 25487: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25487: 0.0001070499420166 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                   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[suppress_filters] => \n            [cache_results] => 1\n            [update_post_term_cache] => 1\n            [update_menu_item_cache] => \n            [lazy_load_term_meta] => 1\n            [update_post_meta_cache] => 1\n            [nopaging] => 1\n            [comments_per_page] => 50\n            [no_found_rows] => \n            [taxonomy] => link_library_category\n            [term_id] => 1128\n            [order] => DESC\n        )\n\n    [tax_query] => WP_Tax_Query Object\n        (\n            [queries] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [terms] => Array\n                                (\n                                    [0] => 1128\n                                )\n\n                            [field] => term_id\n                            [operator] => IN\n                            [include_children] => \n                        )\n\n                )\n\n            [relation] => AND\n            [table_aliases:protected] => Array\n                (\n                    [0] => wp_term_relationships\n                )\n\n            [queried_terms] => Array\n                (\n                    [link_library_category] => Array\n                        (\n                            [terms] => Array\n                                (\n                                    [0] => 1128\n                                )\n\n                            [field] => term_id\n                        )\n\n                )\n\n            [primary_table] => wp_posts\n            [primary_id_column] => ID\n        )\n\n    [meta_query] => WP_Meta_Query Object\n        (\n            [queries] => Array\n                (\n                )\n\n            [relation] => \n            [meta_table] => \n            [meta_id_column] => \n            [primary_table] => \n            [primary_id_column] => \n            [table_aliases:protected] => Array\n                (\n                )\n\n            [clauses:protected] => Array\n                (\n                )\n\n            [has_or_relation:protected] => \n        )\n\n    [date_query] => \n    [request] => \n\t\t\tSELECT   wp_posts.*\n\t\t\tFROM wp_posts  LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1128)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 24012\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:47\n                    [post_date_gmt] => 2022-11-22 09:25:47\n                    [post_content] => \n                    [post_title] => AlphaImpute\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alphaimpute\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:23:25\n                    [post_modified_gmt] => 2025-05-21 05:23:25\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/alphaimpute\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 24159\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:56\n                    [post_date_gmt] => 2022-11-22 09:25:56\n                    [post_content] => \n                    [post_title] => bgc\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bgc\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:37:31\n                    [post_modified_gmt] => 2025-05-21 05:37:31\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bgc\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 26186\n                    [post_author] => 5\n                    [post_date] => 2026-01-05 08:59:54\n                    [post_date_gmt] => 2026-01-05 07:59:54\n                    [post_content] => \n                    [post_title] => BOLT-LMM\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bolt-lmm\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-02-11 10:18:37\n                    [post_modified_gmt] => 2026-02-11 09:18:37\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26186\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 26103\n                    [post_author] => 5\n                    [post_date] => 2025-09-23 06:11:52\n                    [post_date_gmt] => 2025-09-23 04:11:52\n                    [post_content] => \n                    [post_title] => coevol\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => coevol\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-12-17 13:51:32\n                    [post_modified_gmt] => 2025-12-17 12:51:32\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26103\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [4] => WP_Post Object\n                (\n                    [ID] => 24206\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:53\n                    [post_date_gmt] => 2022-11-22 09:25:53\n                    [post_content] => \n                    [post_title] => Eagle\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => eagle\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 13:59:36\n                    [post_modified_gmt] => 2025-05-21 11:59:36\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/eagle\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [5] => WP_Post Object\n                (\n                    [ID] => 25060\n                    [post_author] => 5\n                    [post_date] => 2023-10-04 09:20:42\n                    [post_date_gmt] => 2023-10-04 07:20:42\n                    [post_content] => \n                    [post_title] => EMMAX\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => emmax\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2023-12-05 16:07:55\n                    [post_modified_gmt] => 2023-12-05 15:07:55\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25060\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [6] => WP_Post Object\n                (\n                    [ID] => 24226\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:59\n                    [post_date_gmt] => 2022-11-22 09:25:59\n                    [post_content] => \n                    [post_title] => FaST-LMM\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => fast-lmm\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 15:25:44\n                    [post_modified_gmt] => 2025-05-21 13:25:44\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/fast-lmm\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [7] => WP_Post Object\n                (\n                    [ID] => 24235\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:57\n                    [post_date_gmt] => 2022-11-22 09:25:57\n                    [post_content] => \n                    [post_title] => fineRADstructure\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => fineradstructure\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 15:30:53\n                    [post_modified_gmt] => 2025-05-21 13:30:53\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/fineradstructure\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [8] => WP_Post Object\n                (\n                    [ID] => 23830\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:39\n                    [post_date_gmt] => 2022-11-22 09:25:39\n                    [post_content] => \n                    [post_title] => GCTA\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => gcta\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-01-29 10:15:24\n                    [post_modified_gmt] => 2026-01-29 09:15:24\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/gcta\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [9] => WP_Post Object\n                (\n                    [ID] => 23635\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:31\n                    [post_date_gmt] => 2022-11-22 09:25:31\n                    [post_content] => \n                    [post_title] => GEMMA\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => gemma\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 15:35:48\n                    [post_modified_gmt] => 2025-05-21 13:35:48\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/gemma\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [10] => WP_Post Object\n                (\n                    [ID] => 24336\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:13\n                    [post_date_gmt] => 2022-11-22 09:26:13\n                    [post_content] => \n                    [post_title] => KING\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => king\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-07-29 08:16:51\n                    [post_modified_gmt] => 2025-07-29 06:16:51\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/king\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 25316\n                    [post_author] => 5\n                    [post_date] => 2024-03-18 15:04:17\n                    [post_date_gmt] => 2024-03-18 14:04:17\n                    [post_content] => \n                    [post_title] => kmersGWAS\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => kmersgwas\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-28 14:16:49\n                    [post_modified_gmt] => 2024-03-28 13:16:49\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25316\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [12] => WP_Post Object\n                (\n                    [ID] => 24343\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:57\n                    [post_date_gmt] => 2022-11-22 09:25:57\n                    [post_content] => \n                    [post_title] => lcMLkin\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => lcmlkin\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:13:57\n                    [post_modified_gmt] => 2025-05-22 07:13:57\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/lcmlkin\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [13] => WP_Post Object\n                (\n                    [ID] => 24729\n                    [post_author] => 5\n                    [post_date] => 2023-02-13 07:34:46\n                    [post_date_gmt] => 2023-02-13 06:34:46\n                    [post_content] => \n                    [post_title] => Lep-MAP3\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => lep-map3\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:14:51\n                    [post_modified_gmt] => 2025-05-22 07:14:51\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24729\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [14] => WP_Post Object\n                (\n                    [ID] => 25804\n                    [post_author] => 5\n                    [post_date] => 2025-05-15 13:10:01\n                    [post_date_gmt] => 2025-05-15 11:10:01\n                    [post_content] => \n                    [post_title] => loco-pipe\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => loco-pipe\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-06-25 11:38:20\n                    [post_modified_gmt] => 2025-06-25 09:38:20\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25804\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [15] => WP_Post Object\n                (\n                    [ID] => 23961\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 12:19:36\n                    [post_date_gmt] => 2022-11-22 11:19:36\n                    [post_content] => \n                    [post_title] => MACH\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => mach\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:34:52\n                    [post_modified_gmt] => 2025-05-22 07:34:52\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/mach\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [16] => WP_Post Object\n                (\n                    [ID] => 24365\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:10\n                    [post_date_gmt] => 2022-11-22 09:26:10\n                    [post_content] => \n                    [post_title] => MapThin\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => mapthin\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:35:57\n                    [post_modified_gmt] => 2025-05-22 07:35:57\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/mapthin\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [17] => WP_Post Object\n                (\n                    [ID] => 24382\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:53\n                    [post_date_gmt] => 2022-11-22 09:25:53\n                    [post_content] => \n                    [post_title] => Minimac4\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => minimac4\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-11-03 13:28:34\n                    [post_modified_gmt] => 2025-11-03 12:28:34\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/minimac4\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [18] => WP_Post Object\n                (\n                    [ID] => 24448\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:53\n                    [post_date_gmt] => 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id=\"genomic-association-studies\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Genomic association studies<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/alphagenes.roslin.ed.ac.uk\/wp\/software\/alphaimpute\/\" id=\"link-24012\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlphaImpute<\/a>\n<!-- Time to render name section of link id 24012: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AlphaImpute is a software package for imputing and phasing genotype data in diploid populations with pedigree information.<\/p>\n<!-- Time to render link large description section of link id 24012: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24012: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24012: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/bgcsoftware\/\" id=\"link-24159\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bgc<\/a>\n<!-- Time to render name section of link id 24159: 3.0994415283203E-6 --> \n<\/td>\n<td><p>bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci.<\/p>\n<!-- Time to render link large description section of link id 24159: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24159: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24159: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/alkesgroup.broadinstitute.org\/BOLT-LMM\" id=\"link-26186\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BOLT-LMM<\/a>\n<!-- Time to render name section of link id 26186: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The BOLT-LMM software package consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).<\/p>\n<!-- Time to render link large description section of link id 26186: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BOLT-LMM> How to use <\/a>\n<!-- Time to render notes section of link id 26186: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26186: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/bayesiancook\/coevol\" id=\"link-26103\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">coevol<\/a>\n<!-- Time to render name section of link id 26103: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Correlated evolution of substitution rates and quantitative traits.<\/p>\n<!-- Time to render link large description section of link id 26103: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_coevol> How to use <\/a>\n<!-- Time to render notes section of link id 26103: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26103: 0.00017595291137695 --> \n<tr><td><a href=\"https:\/\/data.broadinstitute.org\/alkesgroup\/Eagle\/\" id=\"link-24206\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Eagle<\/a>\n<!-- Time to render name section of link id 24206: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.<\/p>\n<!-- Time to render link large description section of link id 24206: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24206: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24206: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/genome.sph.umich.edu\/wiki\/EMMAX\" id=\"link-25060\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMMAX<\/a>\n<!-- Time to render name section of link id 25060: 2.1457672119141E-6 --> \n<\/td>\n<td><p><b>EMMAX<\/b>\u00a0is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.<\/p>\n<!-- Time to render link large description section of link id 25060: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMMAX> How to use <\/a>\n<!-- Time to render notes section of link id 25060: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25060: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/www.microsoft.com\/en-us\/download\/details.aspx?id=52559\" id=\"link-24226\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FaST-LMM<\/a>\n<!-- Time to render name section of link id 24226: 2.1457672119141E-6 --> \n<\/td>\n<td><p>FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a program for performing genome-wide association studies (GWAS) on large data sets.<\/p>\n<!-- Time to render link large description section of link id 24226: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24226: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24226: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/github.com\/millanek\/fineRADstructure\" id=\"link-24235\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fineRADstructure<\/a>\n<!-- Time to render name section of link id 24235: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A complete, easy to use, and fast population inference package for RAD-seq data.<\/p>\n<!-- Time to render link large description section of link id 24235: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24235: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24235: 0.00012898445129395 --> \n<tr><td><a href=\"https:\/\/yanglab.westlake.edu.cn\/software\/gcta\/#Overview\" id=\"link-23830\" class=\"track_this_link \" rel=\"noopener noreferrer\">GCTA<\/a>\n<!-- Time to render name section of link id 23830: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.<\/p>\n<!-- Time to render link large description section of link id 23830: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCTA> How to use <\/a>\n<!-- Time to render notes section of link id 23830: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23830: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.xzlab.org\/software.html\" id=\"link-23635\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEMMA<\/a>\n<!-- Time to render name section of link id 23635: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS).<\/p>\n<!-- Time to render link large description section of link id 23635: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEMMA> How to use <\/a>\n<!-- Time to render notes section of link id 23635: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23635: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.kingrelatedness.com\" id=\"link-24336\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KING<\/a>\n<!-- Time to render name section of link id 24336: 2.1457672119141E-6 --> \n<\/td>\n<td><p>KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project.<\/p>\n<!-- Time to render link large description section of link id 24336: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KING> How to use <\/a>\n<!-- Time to render notes section of link id 24336: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24336: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/voichek\/kmersGWAS\" id=\"link-25316\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmersGWAS<\/a>\n<!-- Time to render name section of link id 25316: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A library for running k-mers based GWAS.<\/p>\n<!-- Time to render link large description section of link id 25316: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kmersGWAS> How to use <\/a>\n<!-- Time to render notes section of link id 25316: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25316: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/maximum-likelihood-relatedness-estimation\" id=\"link-24343\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lcMLkin<\/a>\n<!-- Time to render name section of link id 24343: 1.9073486328125E-6 --> \n<\/td>\n<td><p>lcMLkin is a C++ program that allows users to infer biological relatedness from low coverage 2nd generation sequencing data<\/p>\n<!-- Time to render link large description section of link id 24343: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24343: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24343: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/lep-map3\" id=\"link-24729\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Lep-MAP3<\/a>\n<!-- Time to render name section of link id 24729: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Lep-MAP3 is a novel and free software for linkage mapping. It can construct linkage maps on very large number of markers and individuals on single or multiple families.<\/p>\n<!-- Time to render link large description section of link id 24729: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Lep-MAP3> How to use <\/a>\n<!-- Time to render notes section of link id 24729: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24729: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/sudmantlab\/loco-pipe\" id=\"link-25804\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">loco-pipe<\/a>\n<!-- Time to render name section of link id 25804: 1.9073486328125E-6 --> \n<\/td>\n<td><p>loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data.<\/p>\n<!-- Time to render link large description section of link id 25804: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_loco-pipe> How to use <\/a>\n<!-- Time to render notes section of link id 25804: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25804: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/csg.sph.umich.edu\/abecasis\/MaCH\/\" id=\"link-23961\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MACH<\/a>\n<!-- Time to render name section of link id 23961: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MACH is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.<\/p>\n<!-- Time to render link large description section of link id 23961: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23961: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23961: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/www.staff.ncl.ac.uk\/richard.howey\/mapthin\/\" id=\"link-24365\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MapThin<\/a>\n<!-- Time to render name section of link id 24365: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Reduce the number of SNPs in a gene marker dense map computed by PLINK. First, by eliminating linked SNPs. Then, by applying different criteria.<\/p>\n<!-- Time to render link large description section of link id 24365: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24365: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24365: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/statgen\/Minimac4\/\" id=\"link-24382\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minimac4<\/a>\n<!-- Time to render name section of link id 24382: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality.<\/p>\n<!-- Time to render link large description section of link id 24382: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minimac4> How to use <\/a>\n<!-- Time to render notes section of link id 24382: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24382: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.haplotype.org\/software.html\" id=\"link-24448\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">piMASS<\/a>\n<!-- Time to render name section of link id 24448: 2.1457672119141E-6 --> \n<\/td>\n<td><p>posterior inference via Model Averaging and Subset Selection: performs genome-wide joint analysis of all SNPs in association with a phenotype.<\/p>\n<!-- Time to render link large description section of link id 24448: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24448: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24448: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/www.cog-genomics.org\/plink\/\" id=\"link-23698\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PLINK<\/a>\n<!-- Time to render name section of link id 23698: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.<\/p>\n<!-- Time to render link large description section of link id 23698: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PLINK> How to use <\/a>\n<!-- Time to render notes section of link id 23698: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23698: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/mgalardini\/pyseer\" id=\"link-25654\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pyseer<\/a>\n<!-- Time to render name section of link id 25654: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Sequence Element Enrichment Analysis (SEER), python implementation. Pyseer uses linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population on a phenotype of interest, while accounting for potentially very strong confounding population structure. This allows for genome-wide association studies (GWAS) to be performed in clonal organisms such as bacteria and viruses.<\/p>\n<!-- Time to render link large description section of link id 25654: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pyseer> How to use <\/a>\n<!-- Time to render notes section of link id 25654: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25654: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/rgcgithub.github.io\/regenie\/\" id=\"link-26198\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">regenie<\/a>\n<!-- Time to render name section of link id 26198: 1.0013580322266E-5 --> \n<\/td>\n<td><p>regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.<\/p>\n<!-- Time to render link large description section of link id 26198: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_regenie> How to use <\/a>\n<!-- Time to render notes section of link id 26198: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26198: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/AdmiralenOla\/Scoary\" id=\"link-24512\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scoary<\/a>\n<!-- Time to render name section of link id 24512: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits.<\/p>\n<!-- Time to render link large description section of link id 24512: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Scoary> How to use <\/a>\n<!-- Time to render notes section of link id 24512: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24512: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/biocore-ntnu\/snpflip\" id=\"link-25984\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snpflip<\/a>\n<!-- Time to render name section of link id 25984: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Report reverse and ambiguous strand SNPs in GWAS data.<\/p>\n<!-- Time to render link large description section of link id 25984: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_snpflip> How to use <\/a>\n<!-- Time to render notes section of link id 25984: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25984: 0.00011682510375977 --> \n<tr><td><a href=\"http:\/\/www.maizegenetics.net\/tassel\" id=\"link-23748\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TASSEL<\/a>\n<!-- Time to render name section of link id 23748: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Trait Analysis by aSSociation, Evolution and Linkage. TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization for large sets of data.<\/p>\n<!-- Time to render link large description section of link id 23748: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TASSEL> How to use <\/a>\n<!-- Time to render notes section of link id 23748: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23748: 0.00012302398681641 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1146\n                 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class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/gitlab.com\/psc_santos\/ACACIA\" id=\"link-25395\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ACACIA<\/a>\n<!-- Time to render name section of link id 25395: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Allele CAlling proCedure for Illumina Amplicon sequencing data: This workflow aims at extracting allele information out of paired-end Illumina FASTQC files.<\/p>\n<!-- Time to render link large description section of link id 25395: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ACACIA> How to use <\/a>\n<!-- Time to render notes section of link id 25395: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25395: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/sixthresearcher\/amplisat\" id=\"link-25403\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AmpliSAT<\/a>\n<!-- Time to render name section of link id 25403: 2.1457672119141E-6 --> \n<\/td>\n<td><p>AmpliSAT (Amplicon Sequencing Analysis Tools) are a set of online tools that make easy the analysis of Amplicon Sequencing experiments.<\/p>\n<!-- Time to render link large description section of link id 25403: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AmpliSAT> How to use <\/a>\n<!-- Time to render notes section of link id 25403: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25403: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/faculty.washington.edu\/browning\/beagle_utilities\/utilities.html\" id=\"link-24987\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle_Utilities<\/a>\n<!-- Time to render name section of link id 24987: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Simple utility programs for manipulating text files, especially VCF files.<\/p>\n<!-- Time to render link large description section of link id 24987: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24987: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24987: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/single-cell-genetics\/cellsnp-lite\" id=\"link-25928\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cellsnp-lite<\/a>\n<!-- Time to render name section of link id 25928: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cellsnp-lite is a C\/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs.<\/p>\n<!-- Time to render link large description section of link id 25928: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cellsnp-lite> How to use <\/a>\n<!-- Time to render notes section of link id 25928: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25928: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/cgmlstfinder\" id=\"link-24174\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cgMLSTFinder<\/a>\n<!-- Time to render name section of link id 24174: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Core genome Multi-Locus Sequence Typing cgMLSTFinder runs KMA <1> against a chosen core genome MLST (cgMLST) database and outputs the detected alleles in a matrix file.<\/p>\n<!-- Time to render link large description section of link id 24174: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24174: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24174: 0.0001227855682373 --> \n<tr><td><a href=\"https:\/\/github.com\/B-UMMI\/chewBBACA\" id=\"link-26081\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chewBBACA<\/a>\n<!-- Time to render name section of link id 26081: 1.9073486328125E-6 --> \n<\/td>\n<td><p><strong>chewBBACA<\/strong>\u00a0is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg\/wgMLST) schemas and results. The \"BBACA\" stands for \"BSR-Based Allele Calling Algorithm\". BSR stands for BLAST Score Ratio as proposed by\u00a0<a href=\"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-2\" rel=\"nofollow\">Rasko DA et al.<\/a>. The \"chew\" part adds extra coolness to the name and could be thought of as \"Comprehensive and Highly Efficient Workflow\".<\/p>\n<!-- Time to render link large description section of link id 26081: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chewBBACA> How to use <\/a>\n<!-- Time to render notes section of link id 26081: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26081: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/GenisGE\/evalAdmix\" id=\"link-25466\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">evalAdmix<\/a>\n<!-- Time to render name section of link id 25466: 2.1457672119141E-6 --> \n<\/td>\n<td><p>evalAdmix allows to evaluate the results of an admixture analysis (i.e. the result of applying ADMIXTURE, STRUCTURE, NGSadmix and similar).<\/p>\n<!-- Time to render link large description section of link id 25466: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_evalAdmix> How to use <\/a>\n<!-- Time to render notes section of link id 25466: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25466: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/bioinformaticshome.com\/tools\/imputation\/descriptions\/fastPHASE.html\" id=\"link-24230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastPHASE<\/a>\n<!-- Time to render name section of link id 24230: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for genotype imputation and estimating missing haplotypes.<\/p>\n<!-- Time to render link large description section of link id 24230: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24230: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24230: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/browning-lab\/flare\" id=\"link-25560\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">flare<\/a>\n<!-- Time to render name section of link id 25560: 1.9073486328125E-6 --> \n<\/td>\n<td>The flare program uses a set of reference haplotypes to infer the ancestry of each allele in a set of admixed study samples. The flare program is fast, accurate, and memory-efficient.\n<!-- Time to render link large description section of link id 25560: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_flare> How to use <\/a>\n<!-- Time to render notes section of link id 25560: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25560: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/odelaneau.github.io\/GLIMPSE\/index.html\" id=\"link-24258\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GLIMPSE<\/a>\n<!-- Time to render name section of link id 24258: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.<\/p>\n<!-- Time to render link large description section of link id 24258: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GLIMPSE> How to use <\/a>\n<!-- Time to render notes section of link id 24258: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24258: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/graphtyper\" id=\"link-24263\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">graphtyper<\/a>\n<!-- Time to render name section of link id 24263: 2.1457672119141E-6 --> \n<\/td>\n<td><p>graphtyper is a graph-based variant caller capable of genotyping population-scale short read data sets.<\/p>\n<!-- Time to render link large description section of link id 24263: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_graphtyper> How to use <\/a>\n<!-- Time to render notes section of link id 24263: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24263: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/kr-colab\/locator\" id=\"link-24352\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">locator<\/a>\n<!-- Time to render name section of link id 24352: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A supervised machine learning method for predicting the geographic origin of a sample from genotype or sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24352: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_locator> How to use <\/a>\n<!-- Time to render notes section of link id 24352: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24352: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/LRez\" id=\"link-24357\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRez<\/a>\n<!-- Time to render name section of link id 24357: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Standalone tool and library allowing to work with barcoded linked-reads.<\/p>\n<!-- Time to render link large description section of link id 24357: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24357: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24357: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/caleblareau\/mgatk\" id=\"link-25397\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mgatk<\/a>\n<!-- Time to render name section of link id 25397: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A mitochondrial genome analysis toolkit.<\/p>\n<!-- Time to render link large description section of link id 25397: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mgatk> How to use <\/a>\n<!-- Time to render notes section of link id 25397: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25397: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/eblerjana\/pangenie\" id=\"link-24960\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanGenie<\/a>\n<!-- Time to render name section of link id 24960: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph.<\/p>\n<!-- Time to render link large description section of link id 24960: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanGenie> How to use <\/a>\n<!-- Time to render notes section of link id 24960: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24960: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/pixy.readthedocs.io\/en\/latest\/about.html\" id=\"link-25559\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pixy<\/a>\n<!-- Time to render name section of link id 25559: 2.1457672119141E-6 --> \n<\/td>\n<td>pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (\u03c0) and between (dxy) populations from a VCF.\n<!-- Time to render link large description section of link id 25559: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pixy> How to use <\/a>\n<!-- Time to render notes section of link id 25559: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25559: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/tguenther\/read\/src\/master\/\" id=\"link-25146\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">READ<\/a>\n<!-- Time to render name section of link id 25146: 1.9073486328125E-6 --> \n<\/td>\n<td><p>READ is a method to infer the degree of relationship (up to second degree, i.e. nephew\/niece-uncle\/aunt, grandparent-grandchild or half-siblings) for a pair of low-coverage individuals.<\/p>\n<!-- Time to render link large description section of link id 25146: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_READ> How to use <\/a>\n<!-- Time to render notes section of link id 25146: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25146: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/sex-det\/sdpop\" id=\"link-25703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SDpop<\/a>\n<!-- Time to render name section of link id 25703: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SDpop infers sex-linkage from genotyping data of several individuals of both sexes, collected in panmictic populations.<\/p>\n<!-- Time to render link large description section of link id 25703: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SDpop> How to use <\/a>\n<!-- Time to render notes section of link id 25703: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25703: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/rwdavies\/STITCH\" id=\"link-24543\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STITCH<\/a>\n<!-- Time to render name section of link id 24543: 1.9073486328125E-6 --> \n<\/td>\n<td><p>STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation.<\/p>\n<!-- Time to render link large description section of link id 24543: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24543: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24543: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/llecompte\/SVJedi\" id=\"link-24552\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi<\/a>\n<!-- Time to render name section of link id 24552: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SVJedi is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24552: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24552: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24552: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/SandraLouise\/SVJedi-graph\" id=\"link-24752\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi-graph<\/a>\n<!-- Time to render name section of link id 24752: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SVJedi-graph is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24752: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVJedi-graph> How to use <\/a>\n<!-- Time to render notes section of link id 24752: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24752: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/mourisl\/T1K\" id=\"link-26025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T1K<\/a>\n<!-- Time to render name section of link id 26025: 1.9073486328125E-6 --> \n<\/td>\n<td><p>T1K (The ONE genotyper for Kir and HLA) is a computational tool to infer the alleles for the polymorphic genes such as KIR and HLA. T1K calculates the allele abundances based on the RNA-seq\/WES\/WGS read alignments on the provided allele reference sequences. The abundances are used to pick the true alleles for each gene. T1K provides the post analysis steps, including novel SNP detection and single-cell representation. T1K supports both single-end and paired-end sequencing data with any read length.<\/p>\n<!-- Time to render link large description section of link id 26025: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_T1K> How to use <\/a>\n<!-- Time to render notes section of link id 26025: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26025: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/JiaoLab2021\/varigraph\" id=\"link-26195\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">varigraph<\/a>\n<!-- Time to render name section of link id 26195: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes.<\/p>\n<!-- Time to render link large description section of link id 26195: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_varigraph> How to use <\/a>\n<!-- Time to render notes section of link id 26195: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26195: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/bmvdgeijn\/WASP\" id=\"link-25991\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WASP<\/a>\n<!-- Time to render name section of link id 25991: 2.1457672119141E-6 --> \n<\/td>\n<td><p>WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs.<\/p>\n<!-- Time to render link large description section of link id 25991: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WASP> How to use <\/a>\n<!-- Time to render notes section of link id 25991: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25991: 0.00010895729064941 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    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query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00090503692626953-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1147 level0\"><!-- Div Category --><div id=\"haplotypes\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Haplotypes<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"http:\/\/faculty.washington.edu\/browning\/beagle_utilities\/utilities.html\" id=\"link-24987\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle_Utilities<\/a>\n<!-- Time to render name section of link id 24987: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Simple utility programs for manipulating text files, especially VCF files.<\/p>\n<!-- Time to render link large description section of link id 24987: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24987: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24987: 0.00013017654418945 --> \n<tr><td><a href=\"https:\/\/people.maths.bris.ac.uk\/~madjl\/finestructure-old\/chromopainter_info.html\" id=\"link-24646\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ChromoPainter<\/a>\n<!-- Time to render name section of link id 24646: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ChromoPainter is a tool for finding haplotypes in sequence data.<\/p>\n<!-- Time to render link large description section of link id 24646: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chromopainter> How to use <\/a>\n<!-- Time to render notes section of link id 24646: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24646: 0.00017809867858887 --> \n<tr><td><a href=\"https:\/\/bioinformaticshome.com\/tools\/imputation\/descriptions\/fastPHASE.html\" id=\"link-24230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastPHASE<\/a>\n<!-- Time to render name section of link id 24230: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for genotype imputation and estimating missing haplotypes.<\/p>\n<!-- Time to render link large description section of link id 24230: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24230: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24230: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/browning-lab\/flare\" id=\"link-25560\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">flare<\/a>\n<!-- Time to render name section of link id 25560: 2.1457672119141E-6 --> \n<\/td>\n<td>The flare program uses a set of reference haplotypes to infer the ancestry of each allele in a set of admixed study samples. The flare program is fast, accurate, and memory-efficient.\n<!-- Time to render link large description section of link id 25560: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_flare> How to use <\/a>\n<!-- Time to render notes section of link id 25560: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25560: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/hap.py\" id=\"link-25190\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hap.py<\/a>\n<!-- Time to render name section of link id 25190: 2.1457672119141E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25190: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hap.py> How to use <\/a>\n<!-- Time to render notes section of link id 25190: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25190: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/zengxiaofei\/HapHiC\" id=\"link-26013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HapHiC<\/a>\n<!-- Time to render name section of link id 26013: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HapHiC is an allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules.<\/p>\n<!-- Time to render link large description section of link id 26013: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HapHiC> How to use <\/a>\n<!-- Time to render notes section of link id 26013: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26013: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/Nobel-Justin\/HaploHiC\" id=\"link-24272\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HaploHiC<\/a>\n<!-- Time to render name section of link id 24272: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Comprehensive haplotype division of Hi-C PE-reads based on local contacts ratio.<\/p>\n<!-- Time to render link large description section of link id 24272: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24272: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24272: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/dmarnetto\/haplostrips\/src\/master\/\" id=\"link-25020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haplostrips<\/a>\n<!-- Time to render name section of link id 25020: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Haplostrips produce plots that depict variants in a genomic window among different samples. Visualize similarities between haplotypes with respect to a reference haplotype through haplotype clustering and sorting, useful for revealing hidden population structure.<\/p>\n<!-- Time to render link large description section of link id 25020: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Haplostrips> How to use <\/a>\n<!-- Time to render notes section of link id 25020: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25020: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/www.broadinstitute.org\/haploview\/haploview\" id=\"link-24273\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haploview<\/a>\n<!-- Time to render name section of link id 24273: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.<\/p>\n<!-- Time to render link large description section of link id 24273: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24273: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24273: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/pdimens\/harpy\" id=\"link-25672\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">harpy<\/a>\n<!-- Time to render name section of link id 25672: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.<\/p>\n<!-- Time to render link large description section of link id 25672: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_harpy> How to use <\/a>\n<!-- Time to render notes section of link id 25672: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25672: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/github.com\/AbeelLab\/hat\" id=\"link-24276\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HAT-phasing<\/a>\n<!-- Time to render name section of link id 24276: 3.0994415283203E-6 --> \n<\/td>\n<td><p>HAT is a haplotype assembly tool that use NGS and TGS data along a reference genome to reconstruct haplotypes.<\/p>\n<!-- Time to render link large description section of link id 24276: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24276: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24276: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/peterbeerli.com\/migrate-html5\/index.html\" id=\"link-25550\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Migrate<\/a>\n<!-- Time to render name section of link id 25550: 1.9073486328125E-6 --> \n<\/td>\n<td>Migrate estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture.\n<!-- Time to render link large description section of link id 25550: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Migrate> How to use <\/a>\n<!-- Time to render notes section of link id 25550: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25550: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/OmarOakheart\/nPhase\" id=\"link-24419\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nPhase<\/a>\n<!-- Time to render name section of link id 24419: 1.9073486328125E-6 --> \n<\/td>\n<td><p>nPhase is a ploidy agnostic tool developed in python which predicts the haplotypes of a sample that was sequenced by both long and short reads by aligning them to a reference. It should work with any ploidy.<\/p>\n<!-- Time to render link large description section of link id 24419: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24419: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24419: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/bmda.dmi.unibas.ch\/software.html\" id=\"link-24460\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PredictHaplo<\/a>\n<!-- Time to render name section of link id 24460: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This software aims at reconstructing haplotypes from next-generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24460: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PredictHaplo> How to use <\/a>\n<!-- Time to render notes section of link id 24460: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24460: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/tguenther\/read\/src\/master\/\" id=\"link-25146\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">READ<\/a>\n<!-- Time to render name section of link id 25146: 2.1457672119141E-6 --> \n<\/td>\n<td><p>READ is a method to infer the degree of relationship (up to second degree, i.e. nephew\/niece-uncle\/aunt, grandparent-grandchild or half-siblings) for a pair of low-coverage individuals.<\/p>\n<!-- Time to render link large description section of link id 25146: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_READ> How to use <\/a>\n<!-- Time to render notes section of link id 25146: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25146: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/FelixKrueger\/SNPsplit\" id=\"link-25013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPsplit<\/a>\n<!-- Time to render name section of link id 25013: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SNPsplit is an allele-specific alignment sorter which is designed to read alignment files in SAM\/BAM format and determine the allelic origin of reads that cover known SNP positions.<\/p>\n<!-- Time to render link large description section of link id 25013: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNPsplit> How to use <\/a>\n<!-- Time to render notes section of link id 25013: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25013: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/SunPengChuan\/wgdi\" id=\"link-25319\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WGDI<\/a>\n<!-- Time to render name section of link id 25319: 2.1457672119141E-6 --> \n<\/td>\n<td>WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments.\n<!-- Time to render link large description section of link id 25319: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WGDI> How to use <\/a>\n<!-- Time to render notes section of link id 25319: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25319: 0.00011587142944336 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1141\n     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=> Array\n                (\n                )\n\n            [has_or_relation:protected] => \n        )\n\n    [date_query] => \n    [request] => \n\t\t\tSELECT   wp_posts.*\n\t\t\tFROM wp_posts  LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1141)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 24136\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:54\n                    [post_date_gmt] => 2022-11-22 09:25:54\n                    [post_content] => \n                    [post_title] => ALLHiC\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => allhic\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:23:48\n                    [post_modified_gmt] => 2025-05-21 05:23:48\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/allhic\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 24142\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:05\n                    [post_date_gmt] => 2022-11-22 09:26:05\n                    [post_content] => \n                    [post_title] => Armatus\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => armatus\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:28:14\n                    [post_modified_gmt] => 2025-05-21 05:28:14\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/armatus\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n 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https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25028\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 25594\n                    [post_author] => 5\n                    [post_date] => 2024-12-04 06:55:01\n                    [post_date_gmt] => 2024-12-04 05:55:01\n                    [post_content] => \n                    [post_title] => Chromosight\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => chromosight\n                    [to_ping] => \n                    [pinged] => \n                   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\n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => 8b2ec650b2d6c75feb1f0e0c975c2cda\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0009310245513916-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1141 level0\"><!-- Div Category --><div id=\"hic\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">HiC<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/tangerzhang\/ALLHiC\" id=\"link-24136\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ALLHiC<\/a>\n<!-- Time to render name section of link id 24136: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Phasing and scaffolding polyploid genomes based on Hi-C data<\/p>\n<!-- Time to render link large description section of link id 24136: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ALLHiC> How to use <\/a>\n<!-- Time to render notes section of link id 24136: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24136: 0.00011920928955078 --> \n<tr><td><a href=\"https:\/\/github.com\/kingsfordgroup\/armatus\" id=\"link-24142\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Armatus<\/a>\n<!-- Time to render name section of link id 24142: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Multiresolution domain calling software for chromosome conformation capture interaction matrices. Armatus is a Topologically Associated Domain caller. Follow the Web page to know more about Armatus.<\/p>\n<!-- Time to render link large description section of link id 24142: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24142: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24142: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/Jwindler\/AutoHiC\" id=\"link-25028\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AutoHiC<\/a>\n<!-- Time to render name section of link id 25028: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AutoHiC is a deep learning tool that uses Hi-C data to support genome assembly. It can automatically correct errors during genome assembly and generate genomes at the chromosome level.<\/p>\n<!-- Time to render link large description section of link id 25028: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AutoHiC> How to use <\/a>\n<!-- Time to render notes section of link id 25028: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25028: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/koszullab\/chromosight\" id=\"link-25594\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Chromosight<\/a>\n<!-- Time to render name section of link id 25594: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python package to detect chromatin loops (and other patterns) in Hi-C contact maps.<\/p>\n<!-- Time to render link large description section of link id 25594: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Chromosight> How to use <\/a>\n<!-- Time to render notes section of link id 25594: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25594: 0.00012493133544922 --> \n<tr><td><a href=\"https:\/\/github.com\/open2c\/cooler\" id=\"link-25261\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cooler<\/a>\n<!-- Time to render name section of link id 25261: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.<\/p>\n<!-- Time to render link large description section of link id 25261: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cooler> How to use <\/a>\n<!-- Time to render notes section of link id 25261: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25261: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/Phlya\/coolpuppy\" id=\"link-24186\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">coolpuppy<\/a>\n<!-- Time to render name section of link id 24186: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A versatile tool to perform pile-up analysis on Hi-C data in .cool format.<\/p>\n<!-- Time to render link large description section of link id 24186: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24186: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24186: 0.00012993812561035 --> \n<tr><td><a href=\"https:\/\/github.com\/ykai16\/DARIC\" id=\"link-25116\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DARIC<\/a>\n<!-- Time to render name section of link id 25116: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A complete framework for identifying quantitatively differential compartments from Hi-C and Micro-C data.<\/p>\r\n<p><code>DARIC<\/code>, or Differential Analysis for genomic Regions' Interaction with Compartments, is a computational framework to identify the quantitatively differential compartments from Hi-C-like data. For more details about the design and implementation of the framework, please check our paper published at\u00a0<a href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-023-09675-w\" rel=\"nofollow\">BMC Genomics<\/a>.<\/p>\n<!-- Time to render link large description section of link id 25116: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DARIC> How to use <\/a>\n<!-- Time to render notes section of link id 25116: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25116: 0.00013208389282227 --> \n<tr><td><a href=\"https:\/\/github.com\/phasegenomics\/FALCON-Phase\" id=\"link-24038\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON-Phase<\/a>\n<!-- Time to render name section of link id 24038: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds.<\/p>\n<!-- Time to render link large description section of link id 24038: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24038: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24038: 0.00012087821960449 --> \n<tr><td><a href=\"https:\/\/github.com\/vaquerizaslab\/fanc\" id=\"link-24225\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FAN-C<\/a>\n<!-- Time to render name section of link id 24225: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Framework for the ANalysis of C-like data.<\/p>\n<!-- Time to render link large description section of link id 24225: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FAN-C> How to use <\/a>\n<!-- Time to render notes section of link id 24225: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24225: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/nadegeguiglielmoni\/GraphUnzip\" id=\"link-24702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphUnzip<\/a>\n<!-- Time to render name section of link id 24702: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Unzip assembly graphs with Hi-C data and\/or long reads.<\/p>\n<!-- Time to render link large description section of link id 24702: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24702: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24702: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/zengxiaofei\/HapHiC\" id=\"link-26013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HapHiC<\/a>\n<!-- Time to render name section of link id 26013: 2.8610229492188E-6 --> \n<\/td>\n<td><p>HapHiC is an allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules.<\/p>\n<!-- Time to render link large description section of link id 26013: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HapHiC> How to use <\/a>\n<!-- Time to render notes section of link id 26013: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26013: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/maxplanck-ie\/HiCAssembler\" id=\"link-25725\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HiCAssembler<\/a>\n<!-- Time to render name section of link id 25725: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software to assemble contigs\/scaffolds into chromosomes using Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 25725: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiCAssembler> How to use <\/a>\n<!-- Time to render notes section of link id 25725: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25725: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/hicexplorer.readthedocs.io\/en\/latest\/index.html\" id=\"link-24287\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HiCExplorer<\/a>\n<!-- Time to render name section of link id 24287: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 24287: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiCExplorer> How to use <\/a>\n<!-- Time to render notes section of link id 24287: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24287: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/hickit\" id=\"link-25032\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hickit<\/a>\n<!-- Time to render name section of link id 25032: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Hickit is a set of tools initially developed to process diploid single-cell Hi-C data. It extracts contact pairs from read alignment, identifies phases of contacts overlapping with SNPs of known phases, imputes missing phases, infers the 3D structure of a single cell and visualizes the structure.<\/p>\n<!-- Time to render link large description section of link id 25032: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hickit> How to use <\/a>\n<!-- Time to render notes section of link id 25032: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25032: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/XiaoTaoWang\/HiCLift\" id=\"link-24709\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HiCLift<\/a>\n<!-- Time to render name section of link id 24709: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and efficient tool for converting chromatin interaction data between genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24709: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24709: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24709: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/phasegenomics\/juicebox_scripts\" id=\"link-24333\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">juicebox_scripts<\/a>\n<!-- Time to render name section of link id 24333: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats<\/p>\n<!-- Time to render link large description section of link id 24333: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24333: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24333: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/rwtourdot\/linker\" id=\"link-24348\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Linker<\/a>\n<!-- Time to render name section of link id 24348: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Linker is a suite of C++ tools useful for interpreting long and linked read sequencing of cancer genomes.<\/p>\n<!-- Time to render link large description section of link id 24348: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24348: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24348: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/jzhoulab\/orca\" id=\"link-25547\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Orca<\/a>\n<!-- Time to render name section of link id 25547: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A deep learning sequence modeling framework for multiscale genome structure prediction.<\/p>\n<!-- Time to render link large description section of link id 25547: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Orca> How to use <\/a>\n<!-- Time to render notes section of link id 25547: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25547: 0.0001981258392334 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-tol\/PretextMap\" id=\"link-25528\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PretextMap<\/a>\n<!-- Time to render name section of link id 25528: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps. Full suite of Pretext tools.<\/p>\n<!-- Time to render link large description section of link id 25528: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PretextMap> How to use <\/a>\n<!-- Time to render notes section of link id 25528: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25528: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-tol\/PretextView\" id=\"link-25527\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PretextView<\/a>\n<!-- Time to render name section of link id 25527: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OpenGL Powered Pretext Contact Map Viewer.<\/p>\n<!-- Time to render link large description section of link id 25527: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PretextView> How to use <\/a>\n<!-- Time to render notes section of link id 25527: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25527: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/machinegun\/SALSA\" id=\"link-24109\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SALSA<\/a>\n<!-- Time to render name section of link id 24109: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool to scaffold long read assemblies with Hi-C data<\/p>\n<!-- Time to render link large description section of link id 24109: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SALSA> How to use <\/a>\n<!-- Time to render notes section of link id 24109: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24109: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/ay-lab\/selfish\" id=\"link-25259\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SELFISH<\/a>\n<!-- Time to render name section of link id 25259: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.<\/p>\n<!-- Time to render link large description section of link id 25259: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SELFISH> How to use <\/a>\n<!-- Time to render notes section of link id 25259: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25259: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/lihan97\/sslHiC\" id=\"link-25348\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sslHiC<\/a>\n<!-- Time to render name section of link id 25348: 2.1457672119141E-6 --> \n<\/td>\n<td><p>sslHiC is a computational framework for comparative analyses of Hi-C data, including reproducibility measurement and differential chromatin interaction (DCI) detection.<\/p>\n<!-- Time to render link large description section of link id 25348: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sslHiC> How to use <\/a>\n<!-- Time to render notes section of link id 25348: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25348: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/deepomicslab\/SuperTAD\" id=\"link-24549\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SuperTAD<\/a>\n<!-- Time to render name section of link id 24549: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SuperTAD is an open-source command-line TAD detection package written in C++. It takes either raw or normalized Hi-C contact maps as inputs.<\/p>\n<!-- Time to render link large description section of link id 24549: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SuperTAD> How to use <\/a>\n<!-- Time to render notes section of link id 24549: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24549: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/c-zhou\/yahs\" id=\"link-24597\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">YaHS<\/a>\n<!-- Time to render name section of link id 24597: 2.1457672119141E-6 --> \n<\/td>\n<td><p>YaHS is a scaffolding tool using Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 24597: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_YaHS> How to use <\/a>\n<!-- Time to render notes section of link id 24597: 0 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query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00070405006408691-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1137 level0\"><!-- Div Category --><div id=\"iso-seq-analysis\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Iso-seq analysis<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/ANGEL\" id=\"link-24007\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ANGEL<\/a>\n<!-- Time to render name section of link id 24007: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Robust Open Reading Frame prediction (ANGLE re-implementation)<\/p>\n<!-- Time to render link large description section of link id 24007: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24007: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24007: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/kamimrcht\/CARNAC-LR\" id=\"link-24000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CARNAC-LR<\/a>\n<!-- Time to render name section of link id 24000: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Clustering coefficient-based Acquisition of RNA Communities in Long Reads.<\/p>\n<!-- Time to render link large description section of link id 24000: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24000: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24000: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/Magdoll\/cDNA_Cupcake\" id=\"link-23996\" class=\"track_this_link \" rel=\"noopener noreferrer\">cDNA_Cupcake<\/a>\n<!-- Time to render name section of link id 23996: 3.0994415283203E-6 --> \n<\/td>\n<td><p>cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23996: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Cogent module\n<!-- Time to render notes section of link id 23996: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23996: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/Magdoll\/Cogent\" id=\"link-23997\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cogent<\/a>\n<!-- Time to render name section of link id 23997: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.<\/p>\n<!-- Time to render link large description section of link id 23997: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cogent> How to use <\/a>\n<!-- Time to render notes section of link id 23997: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23997: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/IsoSeq\" id=\"link-24328\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IsoSeq<\/a>\n<!-- Time to render name section of link id 24328: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads.<\/p>\n<!-- Time to render link large description section of link id 24328: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IsoSeq> How to use <\/a>\n<!-- Time to render notes section of link id 24328: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24328: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/ConesaLab\/SQANTI3\" id=\"link-24537\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SQANTI3<\/a>\n<!-- Time to render name section of link id 24537: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SQANTI3 is the newest version of the SQANTI tool (publication) that merges features from SQANTI, (code repository) and SQANTI2 (code repository), together with new additions. SQANTI3 will continue as an integrated development aiming to providing you the best characterization possible for your new long read-defined transcriptome. SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, that also includes IsoAnnot and tappAS.<\/p>\n<!-- Time to render link large description section of link id 24537: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24537: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24537: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/GenomeRIK\/tama\" id=\"link-24557\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TAMA<\/a>\n<!-- Time to render name section of link id 24557: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Transcriptome Annotation by Modular Algorithms: this software was designed for processing Iso-Seq data and other long read transcriptome data.<\/p>\n<!-- Time to render link large description section of link id 24557: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TAMA> How to use <\/a>\n<!-- Time to render notes section of link id 24557: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24557: 0.00011014938354492 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1135\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n  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[post_date] => 2022-11-22 10:25:54\n                    [post_date_gmt] => 2022-11-22 09:25:54\n                    [post_content] => \n                    [post_title] => AMAS\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => amas\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:24:27\n                    [post_modified_gmt] => 2025-05-21 05:24:27\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/amas\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    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09:42:43\n                    [post_content] => \n                    [post_title] => art_modern\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => art_modern\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-02-11 10:14:36\n                    [post_modified_gmt] => 2026-02-11 09:14:36\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26188\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            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=> closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => badread\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-02-11 10:16:06\n                    [post_modified_gmt] => 2026-02-11 09:16:06\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26191\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 24152\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:02\n                    [post_date_gmt] => 2022-11-22 09:26:02\n                    [post_content] => \n                    [post_title] => bamaddrg\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bamaddrg\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:32:52\n                    [post_modified_gmt] => 2025-05-21 05:32:52\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bamaddrg\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n       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[ping_status] => closed\n                    [post_password] => \n                    [post_name] => bamtofastq\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:33:46\n                    [post_modified_gmt] => 2025-05-21 05:33:46\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bamtofastq\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [15] => WP_Post Object\n                (\n                    [ID] => 23589\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n       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=> \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => c78ddf7fcb48480a28b13d448d01e47c\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0037670135498047-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1135 level0\"><!-- Div Category --><div id=\"librairies-and-other-tools\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Librairies and other tools<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/NBISweden\/AGAT\" id=\"link-24135\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AGAT<\/a>\n<!-- Time to render name section of link id 24135: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Another Gff Analysis Toolkit: suite of tools to handle gene annotations in any GTF\/GFF format. Some examples what AGAT can do: standardise any GTF\/GFF file into a comprehensive GFF3 format (script with agat_sp prefix): add missing parent features (e.g. gene and mRNA if only CDS\/exon exist). add missing features (e.g. exon and UTR). add missing mandatory attributes (i.e. ID, Parent). fix identifier to be uniq. fix feature location. remove duplicated features. group related features (if spread in different places in the file). sort features. merge overlapping loci into one single locus (only if option activated).<\/p>\n<!-- Time to render link large description section of link id 24135: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AGAT> How to use <\/a>\n<!-- Time to render notes section of link id 24135: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24135: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/refresh-bio\/agc\" id=\"link-26219\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AGC<\/a>\n<!-- Time to render name section of link id 26219: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans).<\/p>\n<!-- Time to render link large description section of link id 26219: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AGC> How to use <\/a>\n<!-- Time to render notes section of link id 26219: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26219: 0.00011420249938965 --> \n<tr><td><a href=\"https:\/\/github.com\/tobiasrausch\/alfred\" id=\"link-23978\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Alfred<\/a>\n<!-- Time to render name section of link id 23978: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BAM Statistics, Feature Counting and Annotation<\/p>\n<!-- Time to render link large description section of link id 23978: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23978: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23978: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/marekborowiec\/AMAS\" id=\"link-24138\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AMAS<\/a>\n<!-- Time to render name section of link id 24138: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Calculate summary statistics and manipulate multiple sequence alignments.<\/p>\n<!-- Time to render link large description section of link id 24138: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24138: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24138: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/apptainer\/apptainer\" id=\"link-25160\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Apptainer<\/a>\n<!-- Time to render name section of link id 25160: 1.9073486328125E-6 --> \n<\/td>\n<td>Apptainer is an open source container platform designed to be simple, fast, and secure.\n<!-- Time to render link large description section of link id 25160: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Apptainer> How to use <\/a>\n<!-- Time to render notes section of link id 25160: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25160: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/skoren\/ArrowGrid\" id=\"link-24144\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ArrowGrid<\/a>\n<!-- Time to render name section of link id 24144: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The distribution is a parallel wrapper around the Arrow consensus framework within the SMRT Analysis Software<\/p>\n<!-- Time to render link large description section of link id 24144: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ArrowGrid> How to use <\/a>\n<!-- Time to render notes section of link id 24144: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24144: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/www.niehs.nih.gov\/research\/resources\/software\/biostatistics\/art\/\" id=\"link-23928\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ART<\/a>\n<!-- Time to render name section of link id 23928: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ART is a set of simulation tools to generate synthetic next-generation sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 23928: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23928: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23928: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/YU-Zhejian\/art_modern\" id=\"link-26188\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">art_modern<\/a>\n<!-- Time to render name section of link id 26188: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A modern re-implementation of the popular ART simulator with enhanced performance and functionality.<\/p>\n<!-- Time to render link large description section of link id 26188: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_art_modern> How to use <\/a>\n<!-- Time to render notes section of link id 26188: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26188: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/kundajelab\/atac_dnase_pipelines\" id=\"link-23874\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">atac dnase pipelines<\/a>\n<!-- Time to render name section of link id 23874: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ATAC-seq and DNase-seq processing pipeline. This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data.<\/p>\n<!-- Time to render link large description section of link id 23874: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23874: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23874: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/docs.aws.amazon.com\/fr_fr\/cli\/latest\/userguide\/getting-started-install.html\" id=\"link-25023\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">awscli<\/a>\n<!-- Time to render name section of link id 25023: 2.1457672119141E-6 --> \n<\/td>\n<td>The AWS Command Line Interface (AWS CLI) is an open source tool that enables you to interact with AWS services using commands in your command-line shell.\n<!-- Time to render link large description section of link id 25023: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_aws> How to use <\/a>\n<!-- Time to render notes section of link id 25023: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25023: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Badread\" id=\"link-26191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Badread<\/a>\n<!-- Time to render name section of link id 26191: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Badread is a long-read simulator tool that makes \u2013 you guessed it \u2013 bad reads! It can imitate many kinds of problems one might encounter in real long-read sets: chimeras, low-quality regions, systematic basecalling errors and more.<\/p>\n<!-- Time to render link large description section of link id 26191: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Badread> How to use <\/a>\n<!-- Time to render notes section of link id 26191: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26191: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/bamaddrg\" id=\"link-24152\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bamaddrg<\/a>\n<!-- Time to render name section of link id 24152: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Adds read groups to input BAM files, streams BAM output on stdout.<\/p>\n<!-- Time to render link large description section of link id 24152: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24152: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24152: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/udall-lab.byu.edu\/Research\/Software\/BamBam.aspx\" id=\"link-23922\" class=\"track_this_link \" rel=\"noopener noreferrer\">BamBam<\/a>\n<!-- Time to render name section of link id 23922: 1.9073486328125E-6 --> \n<\/td>\n<td><p>several simple-to-use tools to facilitate NGS analysis<\/p>\n<!-- Time to render link large description section of link id 23922: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23922: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23922: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/guigolab\/bamstats\" id=\"link-24153\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bamstats (notsame as BAMstats)<\/a>\n<!-- Time to render name section of link id 24153: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bamstats is a command line tool written in Go for computing mapping statistics from a BAM file.<\/p>\n<!-- Time to render link large description section of link id 24153: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24153: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24153: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/10XGenomics\/bamtofastq\" id=\"link-24154\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bamtofastq<\/a>\n<!-- Time to render name section of link id 24154: 9.5367431640625E-7 --> \n<\/td>\n<td><p>Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files.<\/p>\n<!-- Time to render link large description section of link id 24154: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bamtofastq> How to use <\/a>\n<!-- Time to render notes section of link id 24154: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24154: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/pezmaster31\/bamtools\" id=\"link-23589\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bamtools<\/a>\n<!-- Time to render name section of link id 23589: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.<\/p>\n<!-- Time to render link large description section of link id 23589: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bamtools> How to use <\/a>\n<!-- Time to render notes section of link id 23589: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23589: 9.8943710327148E-5 --> \n<tr><td><a href=\"http:\/\/genome.sph.umich.edu\/wiki\/BamUtil\" id=\"link-23590\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bamUtil<\/a>\n<!-- Time to render name section of link id 23590: 1.9073486328125E-6 --> \n<\/td>\n<td><p>bamUtil is a repository that contains several programs that perform operations on SAM\/BAM files. All of these programs are built into a single executable, bam.<\/p>\n<!-- Time to render link large description section of link id 23590: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bamUtil> How to use <\/a>\n<!-- Time to render notes section of link id 23590: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23590: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/bbmap\/\" id=\"link-23785\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BBMap<\/a>\n<!-- Time to render name section of link id 23785: 1.9073486328125E-6 --> \n<\/td>\n<td><p>a short read aligner, as well as various other bioinformatic tools.<\/p>\n<!-- Time to render link large description section of link id 23785: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BBMap> How to use <\/a>\n<!-- Time to render notes section of link id 23785: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23785: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/support.illumina.com\/sequencing\/sequencing_software\/bcl2fastq-conversion-software.html\" id=\"link-23593\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bcl2fastq<\/a>\n<!-- Time to render name section of link id 23593: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The Bcl2FastQ conversion software is a new tool to handle bcl conversion and demultiplexing of both unzipped and zipped bcl files, which have reduced footprint and were introduced as an optional output of the HCS Software version 2.0<\/p>\n<!-- Time to render link large description section of link id 23593: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bcl2fastq> How to use <\/a>\n<!-- Time to render notes section of link id 23593: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23593: 0.00012111663818359 --> \n<tr><td><a href=\"http:\/\/bedops.readthedocs.io\/en\/latest\/index.html\" id=\"link-23865\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BEDOPS<\/a>\n<!-- Time to render name section of link id 23865: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.<\/p>\n<!-- Time to render link large description section of link id 23865: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BEDOPS> How to use <\/a>\n<!-- Time to render notes section of link id 23865: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23865: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/bedtools\/\" id=\"link-23595\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bedtools<\/a>\n<!-- Time to render name section of link id 23595: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.<\/p>\n<!-- Time to render link large description section of link id 23595: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bedtools> How to use <\/a>\n<!-- Time to render notes section of link id 23595: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23595: 0.00013184547424316 --> \n<tr><td><a href=\"http:\/\/pcingola.github.com\/BigDataScript\/\" id=\"link-23934\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BigDataScript<\/a>\n<!-- Time to render name section of link id 23934: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BigDataScript is intended as a scripting language for big data pipeline<\/p>\n<!-- Time to render link large description section of link id 23934: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23934: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23934: 9.4890594482422E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/bioawk\" id=\"link-24687\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bioawk<\/a>\n<!-- Time to render name section of link id 24687: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA\/Q and TAB-delimited formats with column names.<\/p>\n<!-- Time to render link large description section of link id 24687: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bioawk> How to use <\/a>\n<!-- Time to render notes section of link id 24687: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24687: 9.608268737793E-5 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/ustenzel\/biohazard-tools\/src\/master\/\" id=\"link-24113\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">biohazard-tools<\/a>\n<!-- Time to render name section of link id 24113: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This is a collection of command line utilities that do useful stuff involving BAM files for Next Generation Sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24113: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24113: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24113: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/maasha\/biopieces\" id=\"link-24160\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Biopieces<\/a>\n<!-- Time to render name section of link id 24160: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks.<\/p>\n<!-- Time to render link large description section of link id 24160: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24160: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24160: 9.9897384643555E-5 --> \n<tr><td><a href=\"http:\/\/biopython.org\/wiki\/Biopython\" id=\"link-23596\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BIOPYTHON<\/a>\n<!-- Time to render name section of link id 23596: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.<\/p>\n<!-- Time to render link large description section of link id 23596: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.11.1<br> (see &quot;search_Python_module&quot; script <br> to search in others Python versions)\n<!-- Time to render notes section of link id 23596: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23596: 0.00010299682617188 --> \n<tr><td><a href=\"https:\/\/github.com\/lstevens17\/busco2fasta\" id=\"link-25024\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">busco2fasta<\/a>\n<!-- Time to render name section of link id 25024: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A script to turn a set of BUSCO results into a directory of multisequence FASTA files.<\/p>\n<!-- Time to render link large description section of link id 25024: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 25024: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25024: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/CRG-Barcelona\/bwtool\/wiki\" id=\"link-23779\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwtools<\/a>\n<!-- Time to render name section of link id 23779: 1.9073486328125E-6 --> \n<\/td>\n<td><p>bwtool is a command-line utility for bigWig files.<\/p>\n<!-- Time to render link large description section of link id 23779: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23779: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23779: 9.7036361694336E-5 --> \n<tr><td><a href=\"https:\/\/www.haskell.org\/cabal\/\" id=\"link-24112\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cabal<\/a>\n<!-- Time to render name section of link id 24112: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cabal is the standard package system for Haskell software. It helps people to configure, build and install Haskell software and to distribute it easily to other users and developers.<\/p>\n<!-- Time to render link large description section of link id 24112: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24112: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24112: 9.608268737793E-5 --> \n<tr><td><a href=\"http:\/\/ccl.cse.nd.edu\/software\/downloadfiles.php\" id=\"link-23892\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cctools<\/a>\n<!-- Time to render name section of link id 23892: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.<\/p>\n<!-- Time to render link large description section of link id 23892: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23892: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23892: 9.608268737793E-5 --> \n<tr><td><a href=\"http:\/\/cd-hit.org\" id=\"link-23605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cd-hit<\/a>\n<!-- Time to render name section of link id 23605: 3.0994415283203E-6 --> \n<\/td>\n<td><p>CD-HIT stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative.<\/p>\n<!-- Time to render link large description section of link id 23605: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CD-HIT> How to use <\/a>\n<!-- Time to render notes section of link id 23605: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23605: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/cdbfasta\" id=\"link-24172\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cdbfasta<\/a>\n<!-- Time to render name section of link id 24172: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is a brief introduction to a couple of platform independent file-based hashing tools (cdbfasta and cdbyank) that can be used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files.<\/p>\n<!-- Time to render link large description section of link id 24172: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cdbfasta> How to use <\/a>\n<!-- Time to render notes section of link id 24172: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24172: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/circos.ca\/\" id=\"link-23793\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">circos<\/a>\n<!-- Time to render name section of link id 23793: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Circos is a software package for visualizing data and information.<\/p>\n<!-- Time to render link large description section of link id 23793: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Circos> How to use <\/a>\n<!-- Time to render notes section of link id 23793: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23793: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/mschubert\/clustermq\/tree\/develop\" id=\"link-24123\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">clustermq<\/a>\n<!-- Time to render name section of link id 24123: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ClusterMQ: send R function calls as cluster job<\/p>\n<!-- Time to render link large description section of link id 24123: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24123: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24123: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/coder.com\/docs\/code-server\" id=\"link-25652\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">code-server<\/a>\n<!-- Time to render name section of link id 25652: 1.9073486328125E-6 --> \n<\/td>\n<td>Run VSCode on any machine anywhere and access it in the browser.\n<!-- Time to render link large description section of link id 25652: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_code-server> How to use <\/a>\n<!-- Time to render notes section of link id 25652: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25652: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/lilit-nersisyan\/computel\" id=\"link-26019\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Computel<\/a>\n<!-- Time to render name section of link id 26019: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Computel is designed for measuring mean telomere length and abundance of canonical and variant telomeric repeats from Illumina Whole Genome NGS Sequencing data.<\/p>\n<!-- Time to render link large description section of link id 26019: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Computel> How to use <\/a>\n<!-- Time to render notes section of link id 26019: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26019: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/mfbalin\/Concrete-Autoencoders\" id=\"link-24184\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Concrete Autoencoders<\/a>\n<!-- Time to render name section of link id 24184: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The concrete autoencoder is an end-to-end differentiable method for global feature selection, which efficiently identifies a subset of the most informative features and simultaneously learns a neural network to reconstruct the input data from the selected features.<\/p>\n<!-- Time to render link large description section of link id 24184: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24184: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24184: 0.00010204315185547 --> \n<tr><td><a href=\"https:\/\/github.com\/shenwei356\/csvtk\" id=\"link-24696\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">csvtk<\/a>\n<!-- Time to render name section of link id 24696: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A cross-platform, efficient and practical CSV\/TSV toolkit in Golang.<\/p>\n<!-- Time to render link large description section of link id 24696: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24696: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24696: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/shenwei356\/csvtk\" id=\"link-25735\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">csvtk<\/a>\n<!-- Time to render name section of link id 25735: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A cross-platform, efficient and practical CSV\/TSV toolkit in Golang.<\/p>\n<!-- Time to render link large description section of link id 25735: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_csvtk> How to use <\/a>\n<!-- Time to render notes section of link id 25735: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25735: 9.608268737793E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/Integrative-Transcriptomics\/DamageProfiler\" id=\"link-25127\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DamageProfiler<\/a>\n<!-- Time to render name section of link id 25127: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage.<\/p>\r\n<p dir=\"auto\">DamageProfiler calculates damage profiles of mapped reads and provides a graphical as well as text based representation.<\/p>\r\n<p dir=\"auto\">It creates<\/p>\r\n<ul dir=\"auto\">\r\n\t<li>damage plots<\/li>\r\n\t<li>fragment length distribution<\/li>\r\n\t<li>read identity distribution<\/li>\r\n\t<li>base frequency table of reference<\/li>\r\n\t<li>table of different base misincorporations and their occurrences<\/li>\r\n<\/ul>\n<!-- Time to render link large description section of link id 25127: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PGDSpider> How to use <\/a>\n<!-- Time to render notes section of link id 25127: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25127: 0.00012302398681641 --> \n<tr><td><a href=\"https:\/\/github.com\/TomWright\/dasel\" id=\"link-24774\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Dasel<\/a>\n<!-- Time to render name section of link id 24774: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Dasel (short for data-selector) allows you to query and modify data structures using selector strings.<\/p>\n<!-- Time to render link large description section of link id 24774: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24774: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24774: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/www.gnu.org\/software\/datamash\/\" id=\"link-23926\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">datamash<\/a>\n<!-- Time to render name section of link id 23926: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.<\/p>\n<!-- Time to render link large description section of link id 23926: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> default system\n<!-- Time to render notes section of link id 23926: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23926: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/thegenemyers\/DAZZ_DB\" id=\"link-23614\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAZZ_DB<\/a>\n<!-- Time to render name section of link id 23614: 3.0994415283203E-6 --> \n<\/td>\n<td><p>To facilitate the multiple phases of the dazzler assembler, we organize all the read data into what is effectively a \"database\" of the reads and their meta-information.<\/p>\n<!-- Time to render link large description section of link id 23614: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23614: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23614: 0.00012493133544922 --> \n<tr><td><a href=\"https:\/\/github.com\/HIT-ImmunologyLab\/DBSCAN-SWA\/\" id=\"link-24308\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DBSCAN-SWA<\/a>\n<!-- Time to render name section of link id 24308: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An integrated tool for rapid prophage detection and annotation.<\/p>\n<!-- Time to render link large description section of link id 24308: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24308: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24308: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/fidelram\/deepTools\" id=\"link-23866\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">deepTools<\/a>\n<!-- Time to render name section of link id 23866: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tools to process and analyze deep sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23866: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_deepTools> How to use <\/a>\n<!-- Time to render notes section of link id 23866: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23866: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/gatb.inria.fr\/software\/dsk\/\" id=\"link-23954\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DSK<\/a>\n<!-- Time to render name section of link id 23954: 2.1457672119141E-6 --> \n<\/td>\n<td><p>DSK is a k-mer counting software, similar to Jellyfish. DSK supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. DSK can count k-mers of large Illumina datasets on laptops and desktop computers.<\/p>\n<!-- Time to render link large description section of link id 23954: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23954: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23954: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/ecopcr\/wikis\/home\" id=\"link-23616\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ecoPCR<\/a>\n<!-- Time to render name section of link id 23616: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ecoPCR is an electronic PCR software developed by LECAand Helix-Project . It helps you to estimate Barcode primers quality. In conjunction with OBItools, you can postprocess ecoPCR output to compute barcode coverage and barcode speci?city.<\/p>\n<!-- Time to render link large description section of link id 23616: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ecoPCR> How to use <\/a>\n<!-- Time to render notes section of link id 23616: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23616: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/news\/02-06-2014-entrez-direct-released\/\" id=\"link-23825\" class=\"track_this_link \" rel=\"noopener noreferrer\">EDirect<\/a>\n<!-- Time to render name section of link id 23825: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window<\/p>\n<!-- Time to render link large description section of link id 23825: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_Edirect> How to use <\/a>\n<!-- Time to render notes section of link id 23825: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23825: 0.0001220703125 --> \n<tr><td><a href=\"https:\/\/web2.ega-archive.org\/download\/using-ega-download-client\" id=\"link-24076\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EGA_download_client<\/a>\n<!-- Time to render name section of link id 24076: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The EgaDemoClient is a JAVA based data streamer that enables EGA account holders to securely download files and datasets, either through an interactive shell (IS) or using direct command line mode (DCLM).<\/p>\n<!-- Time to render link large description section of link id 24076: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24076: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24076: 0.00011897087097168 --> \n<tr><td><a href=\"http:\/\/egglib.sourceforge.net\" id=\"link-23618\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EggLib<\/a>\n<!-- Time to render name section of link id 23618: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EggLib is a C++\/Python library and program package for evolutionary genetics and genomics.<\/p>\n<!-- Time to render link large description section of link id 23618: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23618: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23618: 0.00012016296386719 --> \n<tr><td><a href=\"http:\/\/eigen.tuxfamily.org\" id=\"link-24022\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Eigen<\/a>\n<!-- Time to render name section of link id 24022: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.<\/p>\n<!-- Time to render link large description section of link id 24022: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24022: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24022: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/emboss.sourceforge.net\/\" id=\"link-23882\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMBOSS<\/a>\n<!-- Time to render name section of link id 23882: 2.8610229492188E-6 --> \n<\/td>\n<td><p>EMBOSS is \"The European Molecular Biology Open Software Suite\". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.<\/p>\n<!-- Time to render link large description section of link id 23882: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMBOSS> How to use <\/a>\n<!-- Time to render notes section of link id 23882: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23882: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/www.ensembl.org\/info\/docs\/api\/index.html\" id=\"link-23764\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ensembl-API<\/a>\n<!-- Time to render name section of link id 23764: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ensembl uses MySQL relational databases to store its information. A comprehensive set of Application Programme Interfaces (APIs) serve as a middle-layer between underlying database schemes and more specific application programmes. The APIs aim to encapsulate the database layout by providing efficient high-level access to data tables and isolate applications from data layout changes. Ensembl's API is written in Perl<\/p>\n<!-- Time to render link large description section of link id 23764: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23764: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23764: 0.00011110305786133 --> \n<tr><td><a href=\"http:\/\/rssf.i2bc.paris-saclay.fr\/Software\/erpin.php\" id=\"link-24216\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">ERPIN<\/a>\n<!-- Time to render name section of link id 24216: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ERPIN (Easy RNA Profile IdentificatioN) is an RNA motif search program developped by Daniel Gautheret and Andr\u00e9 Lambert.<\/p>\n<!-- Time to render link large description section of link id 24216: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24216: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24216: 0.00013494491577148 --> \n<tr><td><a href=\"https:\/\/cgm.sjtu.edu.cn\/eupan\/\" id=\"link-24220\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EUPAN<\/a>\n<!-- Time to render name section of link id 24220: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Toolkit that integrates various software in order to build eukaryotic pangenomes.<\/p>\n<!-- Time to render link large description section of link id 24220: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24220: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24220: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/CBBresearch\/Spouge\/html_ncbi\/html\/fasta\/composition.html\" id=\"link-23991\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTA Composition<\/a>\n<!-- Time to render name section of link id 23991: 1.9073486328125E-6 --> \n<\/td>\n<td><p>finds the overall composition of sequences in a FASTA file<\/p>\n<!-- Time to render link large description section of link id 23991: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTA_Composition> How to use <\/a>\n<!-- Time to render notes section of link id 23991: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23991: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/CBBresearch\/Spouge\/html_ncbi\/html\/software\/program.html?uid=10\" id=\"link-23933\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTA_Length<\/a>\n<!-- Time to render name section of link id 23933: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FASTA Length finds the lengths of sequences in a FASTA file.<\/p>\n<!-- Time to render link large description section of link id 23933: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTA_Length> How to use <\/a>\n<!-- Time to render notes section of link id 23933: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23933: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/linsalrob\/fasta_validator\" id=\"link-25522\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fasta_validator<\/a>\n<!-- Time to render name section of link id 25522: 1.9073486328125E-6 --> \n<\/td>\n<td><p>C code to validate a fasta file.<\/p>\n<!-- Time to render link large description section of link id 25522: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fasta_validator> How to use <\/a>\n<!-- Time to render notes section of link id 25522: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25522: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/fastk-medians\" id=\"link-25442\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastk-medians<\/a>\n<!-- Time to render name section of link id 25442: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of utilities to calculate the median number of times the k-mers in a sequence of interest occur across the whole set.<\/p>\n<!-- Time to render link large description section of link id 25442: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastk-medians> How to use <\/a>\n<!-- Time to render notes section of link id 25442: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25442: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/rostlab.org\/owiki\/index.php\/Fastprofkernel\" id=\"link-24068\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastprofkernel<\/a>\n<!-- Time to render name section of link id 24068: 2.1457672119141E-6 --> \n<\/td>\n<td><p>fastprofkernel is a Debian package that uses an accelerated version of the original profile kernel <1> to automatically train SVM based classification models. It can assign user-defined classes to so far uncharacterized proteins.<\/p>\n<!-- Time to render link large description section of link id 24068: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastprofkernel> How to use <\/a>\n<!-- Time to render notes section of link id 24068: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24068: 0.00012302398681641 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/\" id=\"link-23624\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastQC<\/a>\n<!-- Time to render name section of link id 23624: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Quality Control application for FastQ files. FastQC is an application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report.<\/p>\n<!-- Time to render link large description section of link id 23624: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastQC> How to use <\/a>\n<!-- Time to render notes section of link id 23624: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23624: 0.00011706352233887 --> \n<tr><td><a href=\"http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/\" id=\"link-23627\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTX-Toolkit<\/a>\n<!-- Time to render name section of link id 23627: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA\/FASTQ files preprocessing.<\/p>\n<!-- Time to render link large description section of link id 23627: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTX-Toolkit> How to use <\/a>\n<!-- Time to render notes section of link id 23627: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23627: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/ffmpeg.org\" id=\"link-25643\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FFmpeg<\/a>\n<!-- Time to render name section of link id 25643: 1.9073486328125E-6 --> \n<\/td>\n<td>FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created.\n<!-- Time to render link large description section of link id 25643: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FFmpeg> How to use <\/a>\n<!-- Time to render notes section of link id 25643: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25643: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/fulcrumgenomics\/fgbio\" id=\"link-24040\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fgbio<\/a>\n<!-- Time to render name section of link id 24040: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A set of tools to analyze genomic data with a focus on Next Generation Sequencing.<\/p>\n<!-- Time to render link large description section of link id 24040: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24040: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24040: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/DjampaKozlowski\/FindingOverCovRegions\" id=\"link-24234\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FindingOverCovRegions<\/a>\n<!-- Time to render name section of link id 24234: 2.1457672119141E-6 --> \n<\/td>\n<td><p>FindOverCovRegions.py search for genomic regions with abnormal read coverage (e.g. depth). To do so, this program requieres begraph-like file (e.g. bedtools genomecov per-base reports) where for each position of the genome, the coverage depth is reported (even 0 values).<\/p>\n<!-- Time to render link large description section of link id 24234: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24234: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24234: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/alastair-droop\/fqtools\" id=\"link-23952\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fqtools<\/a>\n<!-- Time to render name section of link id 23952: 1.9073486328125E-6 --> \n<\/td>\n<td><p>fqtools is a software suite for fast processing of FASTQ files; Various file manipulations are supported.<\/p>\n<!-- Time to render link large description section of link id 23952: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23952: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23952: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/gargammel\" id=\"link-23815\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gargammel<\/a>\n<!-- Time to render name section of link id 23815: 3.0994415283203E-6 --> \n<\/td>\n<td><p>gargammel is an ancient DNA simulator<\/p>\n<!-- Time to render link large description section of link id 23815: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gargammel> How to use <\/a>\n<!-- Time to render notes section of link id 23815: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23815: 0.00011920928955078 --> \n<tr><td><a href=\"https:\/\/cloud.google.com\/sdk\/docs\/install?hl=fr\" id=\"link-26217\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gcloud<\/a>\n<!-- Time to render name section of link id 26217: 1.9073486328125E-6 --> \n<\/td>\n<td><p>gcloud CLI is a set of tools for creating and managing Google Cloud resources.<\/p>\n<!-- Time to render link large description section of link id 26217: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gcloud> How to use <\/a>\n<!-- Time to render notes section of link id 26217: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26217: 0.00012707710266113 --> \n<tr><td><a href=\"https:\/\/bioinfo2.ugr.es\/gCluster\/\" id=\"link-25513\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gCluster<\/a>\n<!-- Time to render name section of link id 25513: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The gCluster algorithm is a general clustering method that predicts clusters of any biological word or combination of them, relying only on the DNA sequence and the statistical significance. When using CG as word, gCluster works similarly to CpGcluster, our method to predict CpG islands. More broadly, gCluster has much in common with wordCluster but uses an improved distance model.<\/p>\n<!-- Time to render link large description section of link id 25513: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gCluster> How to use <\/a>\n<!-- Time to render notes section of link id 25513: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25513: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.gdal.org\/\" id=\"link-23789\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GDAL<\/a>\n<!-- Time to render name section of link id 23789: 2.1457672119141E-6 --> \n<\/td>\n<td><p>a translator library for raster and vector geospatial data formats that is released under an X\/MIT style Open Source license by the Open Source Geospatial Foundation.<\/p>\n<!-- Time to render link large description section of link id 23789: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23789: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23789: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/NCI-GDC\/gdc-client\" id=\"link-25622\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gdc-client<\/a>\n<!-- Time to render name section of link id 25622: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The gdc-client provides several convenience functions over the GDC API which provides general download\/upload via HTTPS.<\/p>\n<!-- Time to render link large description section of link id 25622: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gdc-client> How to use <\/a>\n<!-- Time to render notes section of link id 25622: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25622: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/gemlibrary\/\" id=\"link-25030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEM-library<\/a>\n<!-- Time to render name section of link id 25030: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of very optimized tools for indexing\/querying huge genomes\/files.<\/p>\n<!-- Time to render link large description section of link id 25030: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEM-library> How to use <\/a>\n<!-- Time to render notes section of link id 25030: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25030: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/gemtools\/gemtools\" id=\"link-25103\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEM-Tools<\/a>\n<!-- Time to render name section of link id 25103: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.<\/p>\n<!-- Time to render link large description section of link id 25103: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEM-Tools> How to use <\/a>\n<!-- Time to render notes section of link id 25103: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25103: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/schatzlab\/genomescope\" id=\"link-24072\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeScope<\/a>\n<!-- Time to render name section of link id 24072: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Fast genome analysis from unassembled short reads<\/p>\n<!-- Time to render link large description section of link id 24072: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeScope> How to use <\/a>\n<!-- Time to render notes section of link id 24072: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24072: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/genometools.org\/index.html\" id=\"link-23637\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeTools<\/a>\n<!-- Time to render name section of link id 23637: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named \"gt\".<\/p>\n<!-- Time to render link large description section of link id 23637: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenomeTools> How to use <\/a>\n<!-- Time to render notes section of link id 23637: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23637: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/uni-halle\/gerbil\" id=\"link-24250\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gerbil<\/a>\n<!-- Time to render name section of link id 24250: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A basic task in bioinformatics is the counting of k-mers in genome strings.<\/p>\n<!-- Time to render link large description section of link id 24250: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24250: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24250: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/gfatools\" id=\"link-24254\" class=\"track_this_link \" rel=\"noopener noreferrer\">gfatools<\/a>\n<!-- Time to render name section of link id 24254: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA\/BED.<\/p>\n<!-- Time to render link large description section of link id 24254: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gfatools> How to use <\/a>\n<!-- Time to render notes section of link id 24254: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24254: 0.00012707710266113 --> \n<tr><td><a href=\"https:\/\/github.com\/billzt\/gff3sort\" id=\"link-24255\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gff3sort<\/a>\n<!-- Time to render name section of link id 24255: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A Perl Script to sort gff3 files and produce suitable results for tabix tools<\/p>\n<!-- Time to render link large description section of link id 24255: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24255: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24255: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-pathogens\/gff3toembl\" id=\"link-23929\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gff3toembl<\/a>\n<!-- Time to render name section of link id 23929: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI<\/p>\n<!-- Time to render link large description section of link id 23929: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23929: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23929: 0.00012993812561035 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/gffcompare\" id=\"link-24256\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gffcompare<\/a>\n<!-- Time to render name section of link id 24256: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the \u201cquery\u201d files), when compared with a reference annotation (also provided as GFF).<\/p>\n<!-- Time to render link large description section of link id 24256: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gffcompare> How to use <\/a>\n<!-- Time to render notes section of link id 24256: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24256: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/gpertea\/gffread\" id=\"link-24066\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gffread<\/a>\n<!-- Time to render name section of link id 24066: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GFF\/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.<\/p>\n<!-- Time to render link large description section of link id 24066: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gffread> How to use <\/a>\n<!-- Time to render notes section of link id 24066: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24066: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/pachterlab\/gget\" id=\"link-24689\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gget<\/a>\n<!-- Time to render name section of link id 24689: 1.9073486328125E-6 --> \n<\/td>\n<td><p>gget enables efficient querying of genomic reference databases.<\/p>\n<!-- Time to render link large description section of link id 24689: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24689: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24689: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/cli\/cli\" id=\"link-24257\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gh-cli<\/a>\n<!-- Time to render name section of link id 24257: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gh is GitHub on the command line. It brings pull requests, issues, and other GitHub concepts to the terminal next to where you are already working with git and your code.<\/p>\n<!-- Time to render link large description section of link id 24257: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24257: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24257: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/www.haskell.org\/ghc\/\" id=\"link-24111\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GHC<\/a>\n<!-- Time to render name section of link id 24111: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GHC is a state-of-the-art, open source, compiler and interactive environment for the functional language Haskell<\/p>\n<!-- Time to render link large description section of link id 24111: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24111: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24111: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/gradle.org\" id=\"link-26020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gradle<\/a>\n<!-- Time to render name section of link id 26020: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Gradle is the open source build system of choice for Java, Android, and Kotlin developers.<\/p>\n<!-- Time to render link large description section of link id 26020: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gradle> How to use <\/a>\n<!-- Time to render notes section of link id 26020: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26020: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/sourceforge.net\/projects\/biogrinder\/\" id=\"link-23639\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Grinder<\/a>\n<!-- Time to render name section of link id 23639: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.<\/p>\n<!-- Time to render link large description section of link id 23639: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23639: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23639: 0.00011610984802246 --> \n<tr><td><a href=\"http:\/\/www.genemine.org\/gtftools.php\" id=\"link-24267\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GTFtools<\/a>\n<!-- Time to render name section of link id 24267: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GTFtools provides a set of functions to analyze various modes of gene models.<\/p>\n<!-- Time to render link large description section of link id 24267: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GTFtools> How to use <\/a>\n<!-- Time to render notes section of link id 24267: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24267: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/hal2vg\" id=\"link-25449\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hal2vg<\/a>\n<!-- Time to render name section of link id 25449: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Convert HAL to vg-compatible sequence graph.<\/p>\n<!-- Time to render link large description section of link id 25449: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hal2vg> How to use <\/a>\n<!-- Time to render notes section of link id 25449: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25449: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/SegataLab\/hclust2\" id=\"link-25526\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hclust2<\/a>\n<!-- Time to render name section of link id 25526: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.<\/p>\n<!-- Time to render link large description section of link id 25526: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hclust2> How to use <\/a>\n<!-- Time to render notes section of link id 25526: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25526: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/bioconda.github.io\/recipes\/hcluster_sg\/README.html\" id=\"link-23842\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hcluster_sg<\/a>\n<!-- Time to render name section of link id 23842: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A hierarchical clustering software for sparse graphs<\/p>\n<!-- Time to render link large description section of link id 23842: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23842: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23842: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/portal.hdfgroup.org\/display\/HDFVIEW\/HDFView\" id=\"link-24050\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HDFView<\/a>\n<!-- Time to render name section of link id 24050: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HDFView is a visual tool for browsing and editing HDF4 and HDF5 files.<\/p>\n<!-- Time to render link large description section of link id 24050: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24050: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24050: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/kalarikrlab.org\/Software\/HGT-ID.html\" id=\"link-24104\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HGT-ID<\/a>\n<!-- Time to render name section of link id 24104: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An efficient and sensitive program for detecting viral insertion sequences from known viral reference genome in the genome of human cancers.<\/p>\n<!-- Time to render link large description section of link id 24104: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24104: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24104: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/hicexplorer.readthedocs.io\/en\/latest\/index.html\" id=\"link-24287\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HiCExplorer<\/a>\n<!-- Time to render name section of link id 24287: 3.0994415283203E-6 --> \n<\/td>\n<td><p>HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.<\/p>\n<!-- Time to render link large description section of link id 24287: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiCExplorer> How to use <\/a>\n<!-- Time to render notes section of link id 24287: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24287: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/XiaoTaoWang\/HiCLift\" id=\"link-24709\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HiCLift<\/a>\n<!-- Time to render name section of link id 24709: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and efficient tool for converting chromatin interaction data between genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24709: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24709: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24709: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/cmbi\/hssp\" id=\"link-25667\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hssp<\/a>\n<!-- Time to render name section of link id 25667: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Create DSSP and HSSP files. A series of PDB-related databanks for everyday needs.<\/p>\n<!-- Time to render link large description section of link id 25667: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hssp> How to use <\/a>\n<!-- Time to render notes section of link id 25667: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25667: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/kundajelab\/idr\" id=\"link-24691\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IDR<\/a>\n<!-- Time to render name section of link id 24691: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The IDR (Irreproducible Discovery Rate) framework is a uni\ufb01ed approach to measure the reproducibility of \ufb01ndings identi\ufb01ed from replicate experiments and provide highly stable thresholds based on reproducibility.<\/p>\n<!-- Time to render link large description section of link id 24691: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IDR> How to use <\/a>\n<!-- Time to render notes section of link id 24691: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24691: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/andersen-lab\/ivar\" id=\"link-25121\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iVar<\/a>\n<!-- Time to render name section of link id 25121: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Var is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions\/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.<\/p>\n<!-- Time to render link large description section of link id 25121: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_iVar> How to use <\/a>\n<!-- Time to render notes section of link id 25121: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25121: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/mcmc-jags.sourceforge.net\" id=\"link-24330\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JAGS<\/a>\n<!-- Time to render name section of link id 24330: 1.9073486328125E-6 --> \n<\/td>\n<td><p>JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.<\/p>\n<!-- Time to render link large description section of link id 24330: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JAGS> How to use <\/a>\n<!-- Time to render notes section of link id 24330: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24330: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/tanghaibao\/jcvi\" id=\"link-24332\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JCVI<\/a>\n<!-- Time to render name section of link id 24332: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.<\/p>\n<!-- Time to render link large description section of link id 24332: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JCVI> How to use <\/a>\n<!-- Time to render notes section of link id 24332: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24332: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/www.cbcb.umd.edu\/software\/jellyfish\" id=\"link-23766\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jellyfish<\/a>\n<!-- Time to render name section of link id 23766: 1.9073486328125E-6 --> \n<\/td>\n<td><p>JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.<\/p>\n<!-- Time to render link large description section of link id 23766: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Jellyfish> How to use <\/a>\n<!-- Time to render notes section of link id 23766: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23766: 0.0001060962677002 --> \n<tr><td><a href=\"http:\/\/julialang.org\/\" id=\"link-23833\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Julia<\/a>\n<!-- Time to render name section of link id 23833: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library.<\/p>\n<!-- Time to render link large description section of link id 23833: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Julia> How to use <\/a>\n<!-- Time to render notes section of link id 23833: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23833: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/lindenb\/jvarkit\" id=\"link-24334\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jvarkit<\/a>\n<!-- Time to render name section of link id 24334: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Java utilities for Bioinformatics (only requested tools are compiling)<\/p>\n<!-- Time to render link large description section of link id 24334: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24334: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24334: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/www.earlham.ac.uk\/kat-tools\" id=\"link-23955\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KAT<\/a>\n<!-- Time to render name section of link id 23955: 1.9073486328125E-6 --> \n<\/td>\n<td><p>KAT (The K-mer Analysis Toolkit) is a suite of tools that generate, analyse and compare k-mer spectra produced from sequence files.<\/p>\n<!-- Time to render link large description section of link id 23955: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KAT> How to use <\/a>\n<!-- Time to render notes section of link id 23955: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23955: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/kcoss-2021\/KCOSS\" id=\"link-24742\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KCOSS<\/a>\n<!-- Time to render name section of link id 24742: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and space-saving multi-threaded k-mer frequency statistics algorithm<\/p>\n<!-- Time to render link large description section of link id 24742: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24742: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24742: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/ENCODE-DCC\/kentUtils\" id=\"link-23826\" class=\"track_this_link \" rel=\"noopener noreferrer\">kentUtils<\/a>\n<!-- Time to render name section of link id 23826: 2.1457672119141E-6 --> \n<\/td>\n<td><p>UCSC command line bioinformatic utilities<\/p>\n<!-- Time to render link large description section of link id 23826: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kentUtils> How to use <\/a>\n<!-- Time to render notes section of link id 23826: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23826: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/ldenti\/klocate\" id=\"link-24337\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">klocate<\/a>\n<!-- Time to render name section of link id 24337: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Standalone tool based on the bwa index to locate a set of kmers along a reference genome. klocate searches each kmer (full and perfect match) in the index and outputs all positions the kmer maps to (output to sdtout in bed format).<\/p>\n<!-- Time to render link large description section of link id 24337: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24337: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24337: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/ldenti\/kmap\" id=\"link-24338\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmap<\/a>\n<!-- Time to render name section of link id 24338: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Standalone tool based on the bwa index to locate a set of kmers along a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24338: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24338: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24338: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/tlemane\/kmdiff\" id=\"link-24749\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmdiif<\/a>\n<!-- Time to render name section of link id 24749: 2.1457672119141E-6 --> \n<\/td>\n<td><p>kmdiff provides differential k-mers analysis between two populations (control and case). Each population is represented by a set of short-read sequencing. Outputs are differentially represented k-mers between controls and cases.<\/p>\n<!-- Time to render link large description section of link id 24749: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kmdiff> How to use <\/a>\n<!-- Time to render notes section of link id 24749: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24749: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/kmer-counter\" id=\"link-25440\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmer-counter<\/a>\n<!-- Time to render name section of link id 25440: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A fast k-mer counter written in Rust.<\/p>\n<!-- Time to render link large description section of link id 25440: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kmer-counter> How to use <\/a>\n<!-- Time to render notes section of link id 25440: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25440: 0.00012803077697754 --> \n<tr><td><a href=\"https:\/\/github.com\/ChnMasterOG\/KmerGO\" id=\"link-26026\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KmerGO<\/a>\n<!-- Time to render name section of link id 26026: 1.9073486328125E-6 --> \n<\/td>\n<td><p>KmerGO is a user-friendly tool to identify the group-specific sequences on two groups or trait-associated sequences of high throughput sequencing datasets.<\/p>\n<!-- Time to render link large description section of link id 26026: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KmerGO> How to use <\/a>\n<!-- Time to render notes section of link id 26026: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26026: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/jenniferlu717\/KrakenTools\" id=\"link-25601\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KrakenTools<\/a>\n<!-- Time to render name section of link id 25601: 1.9073486328125E-6 --> \n<\/td>\n<td><p>KrakenTools provides individual scripts to analyze Kraken\/Kraken2\/Bracken\/KrakenUniq output files.<\/p>\n<!-- Time to render link large description section of link id 25601: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KrakenTools> How to use <\/a>\n<!-- Time to render notes section of link id 25601: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25601: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/Krona\/wiki\" id=\"link-23653\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Krona<\/a>\n<!-- Time to render name section of link id 23653: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Krona allows hierarchical data to be explored with zoomable pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats.<\/p>\n<!-- Time to render link large description section of link id 23653: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Krona> How to use <\/a>\n<!-- Time to render notes section of link id 23653: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23653: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/faylward\/lastp_aai\" id=\"link-24342\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lastp_aai<\/a>\n<!-- Time to render name section of link id 24342: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A simple Python script for calculating pairwise amino acid identity (AAI) between protein files (extension .faa)<\/p>\n<!-- Time to render link large description section of link id 24342: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24342: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24342: 0.00012803077697754 --> \n<tr><td><a href=\"https:\/\/github.com\/mfranberg\/libplinkio\" id=\"link-24023\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">libplinkio<\/a>\n<!-- Time to render name section of link id 24023: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is a small C and Python library for reading Plink genotype files.<\/p>\n<!-- Time to render link large description section of link id 24023: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_libplinkio> How to use <\/a>\n<!-- Time to render notes section of link id 24023: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24023: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/www.icir.org\/christian\/libstree\/\" id=\"link-24345\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">libstree<\/a>\n<!-- Time to render name section of link id 24345: 2.1457672119141E-6 --> \n<\/td>\n<td><p>libstree is a generic suffix tree implementation, written in C.<\/p>\n<!-- Time to render link large description section of link id 24345: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_libstree> How to use <\/a>\n<!-- Time to render notes section of link id 24345: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24345: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/agshumate\/Liftoff\" id=\"link-24346\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Liftoff<\/a>\n<!-- Time to render name section of link id 24346: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.<\/p>\n<!-- Time to render link large description section of link id 24346: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Liftoff> How to use <\/a>\n<!-- Time to render notes section of link id 24346: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24346: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/llvm.org\/\" id=\"link-23897\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">llvm<\/a>\n<!-- Time to render name section of link id 23897: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.<\/p>\n<!-- Time to render link large description section of link id 23897: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23897: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23897: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/LRez\" id=\"link-24357\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRez<\/a>\n<!-- Time to render name section of link id 24357: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Standalone tool and library allowing to work with barcoded linked-reads.<\/p>\n<!-- Time to render link large description section of link id 24357: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24357: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24357: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/Mash\" id=\"link-25099\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mash<\/a>\n<!-- Time to render name section of link id 25099: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast genome and metagenome distance estimation using MinHash.<\/p>\r\n<p>documentation : <a href=\"https:\/\/mash.readthedocs.io\/en\/latest\/\">Publications \u2014 Mash 2.0 documentation<\/a><\/p>\n<!-- Time to render link large description section of link id 25099: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Mash> How to use <\/a>\n<!-- Time to render notes section of link id 25099: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25099: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/www.megasoftware.net\/\" id=\"link-24370\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEGA-CC<\/a>\n<!-- Time to render name section of link id 24370: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software suite for analyzing DNA and protein sequence data from species and populations.<\/p>\n<!-- Time to render link large description section of link id 24370: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24370: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24370: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/xff.cz\/megatools\/\" id=\"link-25681\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MegaTools<\/a>\n<!-- Time to render name section of link id 25681: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Open-source command line tools for accessing Mega.co.nz cloud storage.<\/p>\n<!-- Time to render link large description section of link id 25681: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Megatools> How to use <\/a>\n<!-- Time to render notes section of link id 25681: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25681: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/metexplore\/met4j\" id=\"link-24713\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Met4j<\/a>\n<!-- Time to render name section of link id 24713: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.<\/p>\n<!-- Time to render link large description section of link id 24713: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24713: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24713: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/MontrealCorpusTools\/Montreal-Forced-Aligner\" id=\"link-25976\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MFA<\/a>\n<!-- Time to render name section of link id 25976: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The Montreal Forced Aligner is a command line utility for performing forced alignment of speech datasets using Kaldi (http:\/\/kaldi-asr.org\/).<\/p>\n<!-- Time to render link large description section of link id 25976: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MFA> How to use <\/a>\n<!-- Time to render notes section of link id 25976: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25976: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/mamba-org\/micromamba-releases\" id=\"link-26230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">micromamba<\/a>\n<!-- Time to render name section of link id 26230: 1.9073486328125E-6 --> \n<\/td>\n<td><p>micromamba is a single-file executable that is statically linked and can be dropped anywhere on the operating to get started with powerful package management and virtual environments.<\/p>\n<!-- Time to render link large description section of link id 26230: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_micromamba> How to use <\/a>\n<!-- Time to render notes section of link id 26230: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26230: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/conda-forge\/miniforge\" id=\"link-25642\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniforge<\/a>\n<!-- Time to render name section of link id 25642: 8.8214874267578E-6 --> \n<\/td>\n<td><p>Miniforge is a minimal installer for Conda specific to conda-forge.<\/p>\n<!-- Time to render link large description section of link id 25642: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniforge> How to use <\/a>\n<!-- Time to render notes section of link id 25642: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25642: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/brentp\/mosdepth\" id=\"link-24065\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mosdepth<\/a>\n<!-- Time to render name section of link id 24065: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast BAM\/CRAM depth calculation for WGS, exome, or targeted sequencing. mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome. mean per-window depth given a window size--as would be used for CNV calling. the mean per-region given a BED file of regions. a distribution of proportion of bases covered at or above a given threshhold for each chromosome and genome-wide. quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20) threshold output to indicate how many bases in each region are covered at the given thresholds. when appropriate, the output files are bgzipped and indexed for ease of use.<\/p>\n<!-- Time to render link large description section of link id 24065: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mosdepth> How to use <\/a>\n<!-- Time to render notes section of link id 24065: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24065: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/arumugamlab\/msamtools\" id=\"link-26027\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msamtools<\/a>\n<!-- Time to render name section of link id 26027: 1.9073486328125E-6 --> \n<\/td>\n<td><p>msamtools provides useful functions that are commonly used in microbiome data analysis, especially when analyzing shotgun metagenomics or metatranscriptomics data.<\/p>\n<!-- Time to render link large description section of link id 26027: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msamtools> How to use <\/a>\n<!-- Time to render notes section of link id 26027: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26027: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/multiqc.info\/\" id=\"link-23822\" class=\"track_this_link \" rel=\"noopener noreferrer\">MultiQC<\/a>\n<!-- Time to render name section of link id 23822: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Aggregate results from bioinformatics analyses across many samples into a single report.<\/p>\n<!-- Time to render link large description section of link id 23822: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MultiQC> How to use <\/a>\n<!-- Time to render notes section of link id 23822: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23822: 0.00011682510375977 --> \n<tr><td><a href=\"http:\/\/www.ks.uiuc.edu\/Research\/namd\/\" id=\"link-23678\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NAMD<\/a>\n<!-- Time to render name section of link id 23678: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.<\/p>\n<!-- Time to render link large description section of link id 23678: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NAMD> How to use <\/a>\n<!-- Time to render notes section of link id 23678: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23678: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoPlot\" id=\"link-23855\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoPlot<\/a>\n<!-- Time to render name section of link id 23855: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Plotting tool for Oxford Nanopore sequencing data and alignments.<\/p>\n<!-- Time to render link large description section of link id 23855: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoPlot> How to use <\/a>\n<!-- Time to render notes section of link id 23855: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23855: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/SethMMorton\/natsort\" id=\"link-24410\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">natsort<\/a>\n<!-- Time to render name section of link id 24410: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Simple yet flexible natural sorting in Python<\/p>\n<!-- Time to render link large description section of link id 24410: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24410: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24410: 0.00011897087097168 --> \n<tr><td><a href=\"ftp:\/\/ftp.ncbi.nih.gov\/toolbox\/ncbi_tools\/\" id=\"link-23886\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_tools<\/a>\n<!-- Time to render name section of link id 23886: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NCBI portable software toolkit<\/p>\n<!-- Time to render link large description section of link id 23886: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_tools> How to use <\/a>\n<!-- Time to render notes section of link id 23886: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23886: 0.00010895729064941 --> \n<tr><td><a href=\"ftp:\/\/ftp.ncbi.nih.gov\/toolbox\/ncbi_tools++\/\" id=\"link-23895\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_tools++<\/a>\n<!-- Time to render name section of link id 23895: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NCBI C++ Toolkit provides free, portable, public domain libraries.<\/p>\n<!-- Time to render link large description section of link id 23895: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_tools++> How to use <\/a>\n<!-- Time to render notes section of link id 23895: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23895: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/ccl.northwestern.edu\/netlogo\/\" id=\"link-24412\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NetLogo<\/a>\n<!-- Time to render name section of link id 24412: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NetLogo is a multi-agent programmable modeling environment.<\/p>\n<!-- Time to render link large description section of link id 24412: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24412: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24412: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/docs.nextcloud.com\/desktop\/3.4\/advancedusage.html\" id=\"link-24413\" class=\"track_this_link \" rel=\"noopener noreferrer\">NextCloudcmd<\/a>\n<!-- Time to render name section of link id 24413: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A command line client that can be used to synchronize Nextcloud files to client machines.<\/p>\n<!-- Time to render link large description section of link id 24413: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24413: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24413: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.nextflow.io\/\" id=\"link-23889\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Nextflow<\/a>\n<!-- Time to render name section of link id 23889: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.<\/p>\n<!-- Time to render link large description section of link id 23889: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Nextflow> How to use <\/a>\n<!-- Time to render notes section of link id 23889: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23889: 0.00013184547424316 --> \n<tr><td><a href=\"https:\/\/ngsutils.org\" id=\"link-24675\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsutils<\/a>\n<!-- Time to render name section of link id 24675: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tools for next-generation sequencing analysis.<\/p>\n<!-- Time to render link large description section of link id 24675: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NGSUtils> How to use <\/a>\n<!-- Time to render notes section of link id 24675: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24675: 0.00012898445129395 --> \n<tr><td><a href=\"http:\/\/numpy.scipy.org\/\" id=\"link-23682\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">numpy<\/a>\n<!-- Time to render name section of link id 23682: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NumPy is a package needed for scientific computing with Python.<\/p>\n<!-- Time to render link large description section of link id 23682: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23682: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23682: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/obitools\/wikis\/home\" id=\"link-23910\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OBITools<\/a>\n<!-- Time to render name section of link id 23910: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OBITools is a set of python programs developed to simplify the manipulation of sequence files in our labs. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.<\/p>\n<!-- Time to render link large description section of link id 23910: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OBITools> How to use <\/a>\n<!-- Time to render notes section of link id 23910: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23910: 0.00012683868408203 --> \n<tr><td><a href=\"https:\/\/openbabel.org\/\" id=\"link-26150\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OpenBabel<\/a>\n<!-- Time to render name section of link id 26150: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Open Babel is a chemical toolbox designed to speak the many languages of chemical data.<\/p>\n<!-- Time to render link large description section of link id 26150: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OpenBabel> How to use <\/a>\n<!-- Time to render notes section of link id 26150: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26150: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/audeering\/opensmile-python\" id=\"link-25646\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">openSMILE<\/a>\n<!-- Time to render name section of link id 25646: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python package for openSMILE (open-source Speech and Music Interpretation by Large-space Extraction).<\/p>\n<!-- Time to render link large description section of link id 25646: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_openSMILE> How to use <\/a>\n<!-- Time to render notes section of link id 25646: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25646: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/pandoc.org\/\" id=\"link-23808\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pandoc<\/a>\n<!-- Time to render name section of link id 23808: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.<\/p>\n<!-- Time to render link large description section of link id 23808: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pandoc> How to use <\/a>\n<!-- Time to render notes section of link id 23808: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23808: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.gnu.org\/software\/parallel\/\" id=\"link-23898\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">parallel<\/a>\n<!-- Time to render name section of link id 23898: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GNU parallel is a shell tool for executing jobs in parallel using one or more computers.<\/p>\n<!-- Time to render link large description section of link id 23898: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> default system\n<!-- Time to render notes section of link id 23898: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23898: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/rvalieris\/parallel-fastq-dump\" id=\"link-24431\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">parallel-fastq-dump<\/a>\n<!-- Time to render name section of link id 24431: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file (see the protip below). This tool speeds up the process by dividing the work into multiple threads.<\/p>\n<!-- Time to render link large description section of link id 24431: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_parallel-fastq-dump> How to use <\/a>\n<!-- Time to render notes section of link id 24431: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24431: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/YannickJadoul\/Parselmouth\" id=\"link-25809\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Parselmouth<\/a>\n<!-- Time to render name section of link id 25809: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Parselmouth aim to provide a complete and Pythonic interface to the internal Praat code.<\/p>\n<!-- Time to render link large description section of link id 25809: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Parselmouth> How to use <\/a>\n<!-- Time to render notes section of link id 25809: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25809: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbtk\" id=\"link-25472\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pbtk<\/a>\n<!-- Time to render name section of link id 25472: 2.1457672119141E-6 --> \n<\/td>\n<td><p dir=\"auto\" style=\"text-align: left\" align=\"center\">PacBio BAM toolkit<\/p>\n<!-- Time to render link large description section of link id 25472: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pbtk> How to use <\/a>\n<!-- Time to render notes section of link id 25472: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25472: 0.00011014938354492 --> \n<tr><td><a href=\"http:\/\/sco.h-its.org\/exelixis\/web\/software\/pear\/index.html\" id=\"link-23783\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PEAR<\/a>\n<!-- Time to render name section of link id 23783: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.<\/p>\n<!-- Time to render link large description section of link id 23783: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PEAR> How to use <\/a>\n<!-- Time to render notes section of link id 23783: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23783: 0.00010776519775391 --> \n<tr><td><a href=\"ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/Pfam\/Tools\/\" id=\"link-24437\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PfamScan<\/a>\n<!-- Time to render name section of link id 24437: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program that searches a FASTA file against a library of Pfam HMMs.<\/p>\n<!-- Time to render link large description section of link id 24437: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PfamScan> How to use <\/a>\n<!-- Time to render notes section of link id 24437: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24437: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/nanoporetech.github.io\/pomoxis\/index.html\" id=\"link-24458\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pomoxis<\/a>\n<!-- Time to render name section of link id 24458: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing.<\/p>\n<!-- Time to render link large description section of link id 24458: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24458: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24458: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/brown.edu\/Research\/Ramachandran_Lab\/projects\/\" id=\"link-23983\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pong<\/a>\n<!-- Time to render name section of link id 23983: 1.9073486328125E-6 --> \n<\/td>\n<td><p>pong is a freely available software package, released by Behr et al. (2016, Bioinformatics), for post-processing output from clustering inference using population genetic data.<\/p>\n<!-- Time to render link large description section of link id 23983: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23983: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23983: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/popoolation2\/\" id=\"link-23930\" class=\"track_this_link \" rel=\"noopener noreferrer\">PoPoolation2<\/a>\n<!-- Time to render name section of link id 23930: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution.<\/p>\n<!-- Time to render link large description section of link id 23930: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PoPoolation2> How to use <\/a>\n<!-- Time to render notes section of link id 23930: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23930: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/packages.debian.org\/jessie\/pp-popularity-contest\" id=\"link-24067\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pp-popularity-contest<\/a>\n<!-- Time to render name section of link id 24067: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The pp-popularity-contest package sets up a cron job that periodically submits the developers anonymous statistics on the usage of Rost Lab prediction methods installed on this system.<\/p>\n<!-- Time to render link large description section of link id 24067: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pp-popularity-contest> How to use <\/a>\n<!-- Time to render notes section of link id 24067: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24067: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/smithlabcode\/preseq\" id=\"link-24461\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">preseq<\/a>\n<!-- Time to render name section of link id 24461: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Software for predicting library complexity and genome coverage in high-throughput sequencing.<\/p>\n<!-- Time to render link large description section of link id 24461: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_preseq> How to use <\/a>\n<!-- Time to render notes section of link id 24461: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24461: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/primer3.org\/\" id=\"link-23699\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Primer3<\/a>\n<!-- Time to render name section of link id 23699: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Primer3 is a widely used program for designing PCR primers (PCR = \"Polymerase Chain Reaction\").<\/p>\n<!-- Time to render link large description section of link id 23699: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Primer3> How to use <\/a>\n<!-- Time to render notes section of link id 23699: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23699: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/prinseq.sourceforge.net\" id=\"link-24027\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PRINSEQ<\/a>\n<!-- Time to render name section of link id 24027: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.<\/p>\n<!-- Time to render link large description section of link id 24027: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PRINSEQ> How to use <\/a>\n<!-- Time to render notes section of link id 24027: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24027: 0.00022101402282715 --> \n<tr><td><a href=\"https:\/\/github.com\/OSGeo\/proj.4\" id=\"link-23790\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROJ4<\/a>\n<!-- Time to render name section of link id 23790: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cartographic Projections Library<\/p>\n<!-- Time to render link large description section of link id 23790: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23790: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23790: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/luidale\/pybam\" id=\"link-25088\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pybam<\/a>\n<!-- Time to render name section of link id 25088: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Very simple, pure python, BAM file reader. If you do not need to use BAM indexes, pybam is probably the fastest and simplest BAM parser out there, particularly if run under PyPy.<\/p>\n<!-- Time to render link large description section of link id 25088: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pybam> How to use <\/a>\n<!-- Time to render notes section of link id 25088: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25088: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/www.jetbrains.com\/pycharm\/\" id=\"link-23890\" class=\"track_this_link \" rel=\"noopener noreferrer\">PyCharm<\/a>\n<!-- Time to render name section of link id 23890: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PyCharm is a dedicated Python and Django IDE providing a wide range of essential tools for Python developers, tightly integrated together to create a convenient environment for productive Python development and Web development.<\/p>\n<!-- Time to render link large description section of link id 23890: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23890: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23890: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/jiaaro\/pydub\" id=\"link-25647\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pydub<\/a>\n<!-- Time to render name section of link id 25647: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Manipulate audio with a simple and easy high level interface.<\/p>\n<!-- Time to render link large description section of link id 25647: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pydub> How to use <\/a>\n<!-- Time to render notes section of link id 25647: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25647: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/www.pypy.org\" id=\"link-24992\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PyPy<\/a>\n<!-- Time to render name section of link id 24992: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast, compliant alternative implementation of Python.<\/p>\n<!-- Time to render link large description section of link id 24992: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PyPy> How to use <\/a>\n<!-- Time to render notes section of link id 24992: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24992: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/alimanfoo\/pysamstats\" id=\"link-26218\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pysamstats<\/a>\n<!-- Time to render name section of link id 26218: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file.<\/p>\n<!-- Time to render link large description section of link id 26218: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pysamstats> How to use <\/a>\n<!-- Time to render notes section of link id 26218: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26218: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/PySlurm\/pyslurm\" id=\"link-24070\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PySlurm<\/a>\n<!-- Time to render name section of link id 24070: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This module provides a low-level Python wrapper around the Slurm C-API using Cython.<\/p>\n<!-- Time to render link large description section of link id 24070: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24070: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24070: 0.00012493133544922 --> \n<tr><td><a href=\"http:\/\/www.cbcb.umd.edu\/software\/quake\/\" id=\"link-23704\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Quake<\/a>\n<!-- Time to render name section of link id 23704: 1.9073486328125E-6 --> \n<\/td>\n<td><div class=\"content\">t Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. &gt;15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections, which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.<\/div>\n<!-- Time to render link large description section of link id 23704: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Quake> How to use <\/a>\n<!-- Time to render notes section of link id 23704: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23704: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/quarto.org\" id=\"link-25413\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Quarto<\/a>\n<!-- Time to render name section of link id 25413: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Quarto is a software that compiles a markdown code to html, pdf, or many other formats. It is a successor of pandoc.<\/p>\n<!-- Time to render link large description section of link id 25413: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Quarto> How to use <\/a>\n<!-- Time to render notes section of link id 25413: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25413: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/cran.r-project.org\/\" id=\"link-23707\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">R<\/a>\n<!-- Time to render name section of link id 23707: 1.9073486328125E-6 --> \n<\/td>\n<td><p>R is \"GNU S\", a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.<\/p>\n<!-- Time to render link large description section of link id 23707: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_R> How to use <\/a>\n<!-- Time to render notes section of link id 23707: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23707: 0.00013279914855957 --> \n<tr><td><a href=\"https:\/\/github.com\/RabbitBio\/RabbitUniq\" id=\"link-24479\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RabbitUniq<\/a>\n<!-- Time to render name section of link id 24479: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Compute unique k-mer faster.<\/p>\n<!-- Time to render link large description section of link id 24479: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24479: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24479: 0.00012779235839844 --> \n<tr><td><a href=\"https:\/\/github.com\/RabbitBio\/RabbitV\" id=\"link-24480\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RabbitV<\/a>\n<!-- Time to render name section of link id 24480: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RabbitV is a highly optimized and practical toolkit for the detection of viruses and microorganisms in sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24480: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24480: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24480: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/Vicky123wzy\/RetroScan\" id=\"link-24494\" class=\"track_this_link \" rel=\"noopener noreferrer\">RetroScan<\/a>\n<!-- Time to render name section of link id 24494: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RetroScan is an easy-to-use tool for retrocopy identification that integrates a series of bioinformatics tools (LAST, BEDtools, ClustalW2, KaKs_Calculator, HISAT2, StringTie, SAMtools and Shiny) and scripts.<\/p>\n<!-- Time to render link large description section of link id 24494: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RetroScan> How to use <\/a>\n<!-- Time to render notes section of link id 24494: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24494: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/BurntSushi\/ripgrep\" id=\"link-25733\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ripgrep<\/a>\n<!-- Time to render name section of link id 25733: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ripgrep is a line-oriented search tool that recursively searches the current directory for a regex pattern.<\/p>\n<!-- Time to render link large description section of link id 25733: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ripgrep> How to use <\/a>\n<!-- Time to render notes section of link id 25733: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25733: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/sanger-pathogens.github.io\/Roary\/\" id=\"link-23809\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Roary<\/a>\n<!-- Time to render name section of link id 23809: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.<\/p>\n<!-- Time to render link large description section of link id 23809: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Roary> How to use <\/a>\n<!-- Time to render notes section of link id 23809: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23809: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/ropebwt2\" id=\"link-25113\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RopeBWT2<\/a>\n<!-- Time to render name section of link id 25113: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 25113: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RopeBWT2> How to use <\/a>\n<!-- Time to render notes section of link id 25113: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25113: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/ternaris\/rosbags\" id=\"link-25900\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rosbags<\/a>\n<!-- Time to render name section of link id 25900: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Rosbags is the pure python library for everything rosbag.<\/p>\n<!-- Time to render link large description section of link id 25900: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rosbags> How to use <\/a>\n<!-- Time to render notes section of link id 25900: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25900: 0.00011706352233887 --> \n<tr><td><a href=\"http:\/\/younglab.wi.mit.edu\/super_enhancer_code.html\" id=\"link-24504\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ROSE<\/a>\n<!-- Time to render name section of link id 24504: 2.1457672119141E-6 --> \n<\/td>\n<td><p>To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)<\/p>\n<!-- Time to render link large description section of link id 24504: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ROSE> How to use <\/a>\n<!-- Time to render notes section of link id 24504: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24504: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/RealTimeGenomics\/rtg-tools\" id=\"link-26164\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RTGTools<\/a>\n<!-- Time to render name section of link id 26164: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RTG Tools is a subset of\u00a0<a href=\"https:\/\/github.com\/RealTimeGenomics\/rtg-core\">RTG Core<\/a>\u00a0that includes several useful utilities for dealing with VCF files and sequence data. Probably the most interesting is the\u00a0<code>vcfeval<\/code>\u00a0command which performs sophisticated comparison of VCF files.<\/p>\n<!-- Time to render link large description section of link id 26164: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RTGTools> How to use <\/a>\n<!-- Time to render notes section of link id 26164: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26164: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.ruby-lang.org\/en\/\" id=\"link-23899\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ruby<\/a>\n<!-- Time to render name section of link id 23899: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A dynamic, open source programming language.<\/p>\n<!-- Time to render link large description section of link id 23899: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ruby> How to use <\/a>\n<!-- Time to render notes section of link id 23899: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23899: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/shenwei356\/rush\" id=\"link-25734\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rush<\/a>\n<!-- Time to render name section of link id 25734: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A cross-platform command-line tool for executing jobs in parallel.<\/p>\n<!-- Time to render link large description section of link id 25734: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rush> How to use <\/a>\n<!-- Time to render notes section of link id 25734: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25734: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/biod\/sambamba\" id=\"link-23917\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sambamba<\/a>\n<!-- Time to render name section of link id 23917: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.<\/p>\n<!-- Time to render link large description section of link id 23917: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sambamba> How to use <\/a>\n<!-- Time to render notes section of link id 23917: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23917: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/tseemann\/samclip\" id=\"link-24508\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samclip<\/a>\n<!-- Time to render name section of link id 24508: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Filter SAM file for soft and hard clipped alignments<\/p>\n<!-- Time to render link large description section of link id 24508: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24508: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24508: 0.00011491775512695 --> \n<tr><td><a href=\"http:\/\/www.genoscope.cns.fr\/externe\/saturn\/\" id=\"link-23960\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Saturn<\/a>\n<!-- Time to render name section of link id 23960: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for assessing the library saturation without any reference genome. .<\/p>\n<!-- Time to render link large description section of link id 23960: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23960: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23960: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.scala-sbt.org\/\" id=\"link-24039\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sbt<\/a>\n<!-- Time to render name section of link id 24039: 1.9073486328125E-6 --> \n<\/td>\n<td><p>sbt is a build tool for Scala, Java, and more.<\/p>\n<!-- Time to render link large description section of link id 24039: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24039: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24039: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.scipy.org\/\" id=\"link-23724\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">scipy<\/a>\n<!-- Time to render name section of link id 23724: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SciPy (pronounced \"Sigh Pie\") is open-source software for mathematics, science, and engineering. The SciPy library depends on Numpy, which provides convenient and fast N-dimensional array manipulation.<\/p>\n<!-- Time to render link large description section of link id 23724: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> In Python modules<\/a>\n<!-- Time to render notes section of link id 23724: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23724: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/szpiech\/selscan\" id=\"link-23725\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">selscan<\/a>\n<!-- Time to render name section of link id 23725: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program to calculate EHH-based scans for positive selection in genomes.<\/p>\n<!-- Time to render link large description section of link id 23725: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_selscan> How to use <\/a>\n<!-- Time to render notes section of link id 23725: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23725: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/seq-lang.org\/\" id=\"link-24514\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Seq<\/a>\n<!-- Time to render name section of link id 24514: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Seq is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C\/C++.<\/p>\n<!-- Time to render link large description section of link id 24514: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Seq> How to use <\/a>\n<!-- Time to render notes section of link id 24514: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24514: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/www.seqan.de\/\" id=\"link-24074\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SeqAn<\/a>\n<!-- Time to render name section of link id 24074: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.<\/p>\n<!-- Time to render link large description section of link id 24074: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SeqAn> How to use <\/a>\n<!-- Time to render notes section of link id 24074: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24074: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/clwgg\/seqfilter\" id=\"link-23964\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqfilter<\/a>\n<!-- Time to render name section of link id 23964: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Filter fasta\/fastq(.gz) files by ID and\/or sequence length<\/p>\n<!-- Time to render link large description section of link id 23964: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23964: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23964: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/telatin\/seqfu2\" id=\"link-25022\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SeqFu<\/a>\n<!-- Time to render name section of link id 25022: 1.9073486328125E-6 --> \n<\/td>\n<td><p dir=\"auto\">A general-purpose program to manipulate and parse information from FASTA\/FASTQ files, supporting gzipped input files. Includes functions to\u00a0<em>interleave<\/em>\u00a0and\u00a0<em>de-interleave<\/em>\u00a0FASTQ files, to\u00a0<em>rename<\/em>\u00a0sequences and to\u00a0<em>count<\/em>\u00a0and print\u00a0<em>statistics<\/em>\u00a0on sequence lengths.<\/p>\n<!-- Time to render link large description section of link id 25022: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SeqFu> How to use <\/a>\n<!-- Time to render notes section of link id 25022: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25022: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/bioinf.shenwei.me\/seqkit\/\" id=\"link-24020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SeqKit<\/a>\n<!-- Time to render name section of link id 24020: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A cross-platform and ultrafast toolkit for FASTA\/Q file manipulation. Common manipulations of FASTA\/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling.<\/p>\n<!-- Time to render link large description section of link id 24020: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SeqKit> How to use <\/a>\n<!-- Time to render notes section of link id 24020: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24020: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/seqtk\" id=\"link-23902\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Seqtk<\/a>\n<!-- Time to render name section of link id 23902: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Toolkit for processing sequences in FASTA\/Q formats<\/p>\n<!-- Time to render link large description section of link id 23902: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Seqtk> How to use <\/a>\n<!-- Time to render notes section of link id 23902: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23902: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/stschiff\/sequenceTools\" id=\"link-24078\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SequenceTools<\/a>\n<!-- Time to render name section of link id 24078: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tools for population genetics on sequencing datas<\/p>\n<!-- Time to render link large description section of link id 24078: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SequenceTools> How to use <\/a>\n<!-- Time to render notes section of link id 24078: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24078: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/bootphon\/shennong\" id=\"link-26030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Shennong<\/a>\n<!-- Time to render name section of link id 26030: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A Python toolbox for speech features extraction.<\/p>\n<!-- Time to render link large description section of link id 26030: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Shennong> How to use <\/a>\n<!-- Time to render notes section of link id 26030: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26030: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/sylabs\/singularity\" id=\"link-24002\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Singularity<\/a>\n<!-- Time to render name section of link id 24002: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Singularity enables users to have full control of their environment. Singularity containers can be used to package entire scientific workflows, software and libraries, and even data.<\/p>\n<!-- Time to render link large description section of link id 24002: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_singularity> How to use <\/a>\n<!-- Time to render notes section of link id 24002: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24002: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/tbenavi1\/smudgeplot\" id=\"link-24073\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Smudgeplots<\/a>\n<!-- Time to render name section of link id 24073: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Inference of ploidy and heterozygosity structure using whole genome sequencing data. This tool extracts heterozygous kmer pairs from kmer dump files (from jellyfish or KMC) and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA \/ (CovA + CovB)). Smudgeplots are computed from raw\/trimmed reads and show the haplotype structure using heterozygous kmer pairs.<\/p>\n<!-- Time to render link large description section of link id 24073: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_smudgeplot> How to use <\/a>\n<!-- Time to render notes section of link id 24073: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24073: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/snakemake\/\" id=\"link-23807\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Snakemake<\/a>\n<!-- Time to render name section of link id 23807: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style.<\/p>\n<!-- Time to render link large description section of link id 23807: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Snakemake> How to use <\/a>\n<!-- Time to render notes section of link id 23807: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23807: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/gigascience\/bgi-soap2\/tree\/master\/tools\/soap.coverage\/2.7.7\" id=\"link-24526\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">soap.coverage<\/a>\n<!-- Time to render name section of link id 24526: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Can calculate sequencing coverage or physical coverage as well as duplication rate and details of specific block for each segments and whole genome by using SOAP, Blat, Blast, BlastZ, mummer and MAQ aligement results with multi-thread. Gzip file supported.<\/p>\n<!-- Time to render link large description section of link id 24526: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24526: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24526: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sourmash.readthedocs.io\/en\/latest\/\" id=\"link-24529\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sourmash<\/a>\n<!-- Time to render name section of link id 24529: 1.9073486328125E-6 --> \n<\/td>\n<td><p>sourmash is a command-line tool and Python library for computing hash sketches from DNA sequences, comparing them to each other, and plotting the results.<\/p>\n<!-- Time to render link large description section of link id 24529: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sourmash> How to use <\/a>\n<!-- Time to render notes section of link id 24529: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24529: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/splatlab\/squeakr\" id=\"link-24538\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">squeakr<\/a>\n<!-- Time to render name section of link id 24538: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Squeakr is a k-mer-counting and multiset-representation system using the recently-introduced counting quotient filter (CQF) Pandey et al. (2017), a feature-rich approximate membership query (AMQ) data structure.<\/p>\n<!-- Time to render link large description section of link id 24538: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24538: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24538: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/software\/squid\/\" id=\"link-23906\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">squid<\/a>\n<!-- Time to render name section of link id 23906: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A C library that is bundled with much of the above software. C function library for sequence analysis.<\/p>\n<!-- Time to render link large description section of link id 23906: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23906: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23906: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Traces\/sra\/sra.cgi?view=doc\" id=\"link-23736\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SRAToolkit<\/a>\n<!-- Time to render name section of link id 23736: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Toolkit to query Short Reads Archive at NCBI<\/p>\n<!-- Time to render link large description section of link id 23736: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SRA-Toolkit> How to use <\/a>\n<!-- Time to render notes section of link id 23736: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23736: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/homonecloco\/subsampler\" id=\"link-24545\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">subsampler<\/a>\n<!-- Time to render name section of link id 24545: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Small tool to subsample fasta and fastq files.<\/p>\n<!-- Time to render link large description section of link id 24545: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24545: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24545: 0.00011777877807617 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/sumaclust\" id=\"link-23973\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sumaclust<\/a>\n<!-- Time to render name section of link id 23973: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast and exact clustering of sequences.<\/p>\n<!-- Time to render link large description section of link id 23973: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sumaclust> How to use <\/a>\n<!-- Time to render notes section of link id 23973: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23973: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/sumatra\/wikis\/home\" id=\"link-23744\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sumatra<\/a>\n<!-- Time to render name section of link id 23744: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Sumatra was developed by the LECA and aims to compute a great deal of sequence similarities in a fast and exact way, based on the length of the Longest Common Subsequence (LCS) between two sequences. Sequence clustering based on similarities is also available through Sumaclust.<\/p>\n<!-- Time to render link large description section of link id 23744: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sumatra> How to use <\/a>\n<!-- Time to render notes section of link id 23744: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23744: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/vbar\/superstring\" id=\"link-24548\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">superstring<\/a>\n<!-- Time to render name section of link id 24548: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Greedy approximation of the shortest common superstring<\/p>\n<!-- Time to render link large description section of link id 24548: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_superstring> How to use <\/a>\n<!-- Time to render notes section of link id 24548: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24548: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/novoic\/surfboard\" id=\"link-26031\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Surfboard<\/a>\n<!-- Time to render name section of link id 26031: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Python package for modern audio feature extraction.<\/p>\n<!-- Time to render link large description section of link id 26031: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Surfboard> How to use <\/a>\n<!-- Time to render notes section of link id 26031: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26031: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/sourceforge.net\/projects\/samtools\/files\/tabix\/\" id=\"link-23746\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">tabix<\/a>\n<!-- Time to render name section of link id 23746: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TAB-delimited file IndeXer. Useful for vcfTools.<\/p>\n<!-- Time to render link large description section of link id 23746: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in bcftools and samtools\n<!-- Time to render notes section of link id 23746: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23746: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/cancerit\/telomerecat\" id=\"link-26023\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Telomerecat<\/a>\n<!-- Time to render name section of link id 26023: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Telomerecat is a tool for estimating the average telomere length (TL) for a paired end, whole genome sequencing (WGS) sample.<\/p>\n<!-- Time to render link large description section of link id 26023: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.9.18\n<!-- Time to render notes section of link id 26023: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26023: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/pypi.org\/project\/telomerehunter\/\" id=\"link-26022\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TelomereHunter<\/a>\n<!-- Time to render name section of link id 26022: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TelomereHunter extracts, sorts and analyses telomeric reads from WGS Data.<\/p>\n<!-- Time to render link large description section of link id 26022: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-2.7.18\n<!-- Time to render notes section of link id 26022: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26022: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/www.tug.org\/texlive\" id=\"link-24561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TexLive<\/a>\n<!-- Time to render name section of link id 24561: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TeX Live is intended to be a straightforward way to get up and running with the TeX document production system.<\/p>\n<!-- Time to render link large description section of link id 24561: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24561: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24561: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/toulbar2\/toulbar2\" id=\"link-24567\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">toulbar2<\/a>\n<!-- Time to render name section of link id 24567: 1.9073486328125E-6 --> \n<\/td>\n<td><p>toulbar2 is an open-source black-box C++ optimizer for cost function networks and discrete additive graphical models. It can read a variety of formats.<\/p>\n<!-- Time to render link large description section of link id 24567: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_toulbar2> How to use <\/a>\n<!-- Time to render notes section of link id 24567: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24567: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/ultralytics\/ultralytics\" id=\"link-26145\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ultralytics<\/a>\n<!-- Time to render name section of link id 26145: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Ultralytics creates cutting-edge, state-of-the-art (SOTA) YOLO models built on years of foundational research in computer vision and AI.<br \/>\r\nInclude SAHI https:\/\/obss.github.io\/sahi\/<\/p>\n<!-- Time to render link large description section of link id 26145: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Ultralytics> How to use <\/a>\n<!-- Time to render notes section of link id 26145: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26145: 0.00054001808166504 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/hoffmanlab\/umap\/src\/default\/\" id=\"link-24573\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Umap<\/a>\n<!-- Time to render name section of link id 24573: 7.1525573730469E-6 --> \n<\/td>\n<td><p>The free umap software package efficiently identifies uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite converted genome (methylome).<\/p>\n<!-- Time to render link large description section of link id 24573: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24573: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24573: 0.00034809112548828 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/unique-kmer-counts\" id=\"link-25441\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">unique-kmer-counts<\/a>\n<!-- Time to render name section of link id 25441: 6.1988830566406E-6 --> \n<\/td>\n<td><p>This program calculates the number of distinct k-mers for each sequence record in a fasta file and divides it by the total number of k-mers in that record.<\/p>\n<!-- Time to render link large description section of link id 25441: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_unique-kmer-counts> How to use <\/a>\n<!-- Time to render notes section of link id 25441: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25441: 0.00033807754516602 --> \n<tr><td><a href=\"https:\/\/github.com\/bacpop\/unitig-caller\" id=\"link-25656\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">unitig-caller<\/a>\n<!-- Time to render name section of link id 25656: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Methods to determine sequence element (unitig) presence\/absence.<\/p>\n<!-- Time to render link large description section of link id 25656: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_unitig-caller> How to use <\/a>\n<!-- Time to render notes section of link id 25656: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25656: 0.0003349781036377 --> \n<tr><td><a href=\"https:\/\/www.rarlab.com\/rar_add.htm\" id=\"link-26120\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">UnRAR<\/a>\n<!-- Time to render name section of link id 26120: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Easily extract RAR files.<\/p>\n<!-- Time to render link large description section of link id 26120: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_UnRAR> How to use <\/a>\n<!-- Time to render notes section of link id 26120: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26120: 0.00033307075500488 --> \n<tr><td><a href=\"https:\/\/github.com\/cc2qe\/vawk\" id=\"link-23839\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vawk<\/a>\n<!-- Time to render name section of link id 23839: 5.9604644775391E-6 --> \n<\/td>\n<td><p>An awk-like VCF parser<\/p>\n<!-- Time to render link large description section of link id 23839: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23839: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23839: 0.00033211708068848 --> \n<tr><td><a href=\"https:\/\/github.com\/AndersenLab\/VCF-kit\" id=\"link-24755\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VCF-kit<\/a>\n<!-- Time to render name section of link id 24755: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Assorted utilities for the variant call format.<\/p>\n<!-- Time to render link large description section of link id 24755: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24755: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24755: 0.00034403800964355 --> \n<tr><td><a href=\"https:\/\/github.com\/vcflib\/vcflib\" id=\"link-24578\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcflib<\/a>\n<!-- Time to render name section of link id 24578: 5.9604644775391E-6 --> \n<\/td>\n<td><p>C++ library and cmdline tools for parsing and manipulating VCF files.<\/p>\n<!-- Time to render link large description section of link id 24578: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcflib> How to use <\/a>\n<!-- Time to render notes section of link id 24578: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24578: 0.00033402442932129 --> \n<tr><td><a href=\"https:\/\/vcftools.github.io\/index.html\" id=\"link-23760\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VCFtools<\/a>\n<!-- Time to render name section of link id 23760: 5.9604644775391E-6 --> \n<\/td>\n<td><p>VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.<\/p>\n<!-- Time to render link large description section of link id 23760: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VCFtools> How to use <\/a>\n<!-- Time to render notes section of link id 23760: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23760: 0.0003509521484375 --> \n<tr><td><a href=\"http:\/\/www.vmatch.de\" id=\"link-24586\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vmatch<\/a>\n<!-- Time to render name section of link id 24586: 7.1525573730469E-6 --> \n<\/td>\n<td><p>A versatile software tool for e\ufb03ciently solving large scale sequence matching tasks.<\/p>\n<!-- Time to render link large description section of link id 24586: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24586: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24586: 0.00035905838012695 --> \n<tr><td><a href=\"https:\/\/alphacephei.com\/vosk\/\" id=\"link-25808\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vosk<\/a>\n<!-- Time to render name section of link id 25808: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Vosk is an offline open source speech recognition toolkit. It enables speech recognition for 20+ languages and dialects.<\/p>\n<!-- Time to render link large description section of link id 25808: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vosk> How to use <\/a>\n<!-- Time to render notes section of link id 25808: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25808: 0.0003509521484375 --> \n<tr><td><a href=\"https:\/\/github.com\/torognes\/vsearch\" id=\"link-23787\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VSEARCH<\/a>\n<!-- Time to render name section of link id 23787: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Versatile open-source tool for metagenomics<\/p>\n<!-- Time to render link large description section of link id 23787: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VSEARCH> How to use <\/a>\n<!-- Time to render notes section of link id 23787: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23787: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/wgsim\" id=\"link-24591\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Wgsim<\/a>\n<!-- Time to render name section of link id 24591: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Wgsim is a small tool for simulating sequence reads from a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24591: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24591: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24591: 0.00013613700866699 --> \n<tr><td><a href=\"https:\/\/github.com\/openai\/whisper\" id=\"link-25644\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Whisper<\/a>\n<!-- Time to render name section of link id 25644: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Whisper is a general-purpose speech recognition model. It is trained on a large dataset of diverse audio and is also a multitasking model that can perform multilingual speech recognition, speech translation, and language identification.<\/p>\n<!-- Time to render link large description section of link id 25644: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Whisper> How to use <\/a>\n<!-- Time to render notes section of link id 25644: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25644: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/Ensembl\/WiggleTools\" id=\"link-23982\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WiggleTools<\/a>\n<!-- Time to render name section of link id 23982: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc).<\/p>\n<!-- Time to render link large description section of link id 23982: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WiggleTools> How to use <\/a>\n<!-- Time to render notes section of link id 23982: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23982: 0.00014519691467285 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1139\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        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class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/dulunar\/3rdChimeraMiner\" id=\"link-25351\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">3rdChimeraMiner<\/a>\n<!-- Time to render name section of link id 25351: 8.1062316894531E-6 --> \n<\/td>\n<td>Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.\n<!-- Time to render link large description section of link id 25351: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_3rdChimeraMiner> How to use <\/a>\n<!-- Time to render notes section of link id 25351: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25351: 0.00036311149597168 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/ANGEL\" id=\"link-24007\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ANGEL<\/a>\n<!-- Time to render name section of link id 24007: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Robust Open Reading Frame prediction (ANGLE re-implementation)<\/p>\n<!-- Time to render link large description section of link id 24007: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24007: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24007: 0.00035285949707031 --> \n<tr><td><a href=\"https:\/\/github.com\/skoren\/ArrowGrid\" id=\"link-24144\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ArrowGrid<\/a>\n<!-- Time to render name section of link id 24144: 4.0531158447266E-6 --> \n<\/td>\n<td><p>The distribution is a parallel wrapper around the Arrow consensus framework within the SMRT Analysis Software<\/p>\n<!-- Time to render link large description section of link id 24144: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ArrowGrid> How to use <\/a>\n<!-- Time to render notes section of link id 24144: 2.1457672119141E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24144: 0.0002138614654541 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Autocycler\" id=\"link-26119\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Autocycler<\/a>\n<!-- Time to render name section of link id 26119: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A tool for generating consensus long-read assemblies for bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 26119: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Autocycler> How to use <\/a>\n<!-- Time to render notes section of link id 26119: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26119: 0.00020790100097656 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Badread\" id=\"link-26191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Badread<\/a>\n<!-- Time to render name section of link id 26191: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Badread is a long-read simulator tool that makes \u2013 you guessed it \u2013 bad reads! It can imitate many kinds of problems one might encounter in real long-read sets: chimeras, low-quality regions, systematic basecalling errors and more.<\/p>\n<!-- Time to render link large description section of link id 26191: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Badread> How to use <\/a>\n<!-- Time to render notes section of link id 26191: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26191: 0.00021195411682129 --> \n<tr><td><a href=\"https:\/\/github.com\/giuliaguidi\/bella\" id=\"link-24108\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BELLA<\/a>\n<!-- Time to render name section of link id 24108: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A computationally-efficient and highly-accurate long-read to long-read aligner and overlapper.<\/p>\n<!-- Time to render link large description section of link id 24108: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24108: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24108: 0.00020813941955566 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/chopper\" id=\"link-25324\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chopper<\/a>\n<!-- Time to render name section of link id 25324: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.<\/p>\r\n<p>chopper is a tool that reunites the now outdated softwares NanoFilt and NanoLyse. It permits to filter QC files and has a faster execution time than NanoFilt and NanoLyse.<\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 25324: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chopper> How to use <\/a>\n<!-- Time to render notes section of link id 25324: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25324: 0.00020885467529297 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfo-biols\/CIRI-long\" id=\"link-24179\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CIRI-long<\/a>\n<!-- Time to render name section of link id 24179: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Circular RNA Identification for Long-Reads Nanopore Sequencing Data.<\/p>\n<!-- Time to render link large description section of link id 24179: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CIRI-long> How to use <\/a>\n<!-- Time to render notes section of link id 24179: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24179: 0.00020623207092285 --> \n<tr><td><a href=\"https:\/\/github.com\/HKU-BAL\/Clair3\" id=\"link-24181\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Clair3<\/a>\n<!-- Time to render name section of link id 24181: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.<\/p>\n<!-- Time to render link large description section of link id 24181: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Clair3> How to use <\/a>\n<!-- Time to render notes section of link id 24181: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24181: 0.00022196769714355 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/CONSENT\" id=\"link-24079\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CONSENT<\/a>\n<!-- Time to render name section of link id 24079: 4.0531158447266E-6 --> \n<\/td>\n<td><p>CONSENT (sCalable self-cOrrectioN of long reads with multiple SEquence alignmeNT) is a self-correction method for long reads.<\/p>\n<!-- Time to render link large description section of link id 24079: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24079: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24079: 0.00020718574523926 --> \n<tr><td><a href=\"https:\/\/github.com\/tjiangHIT\/cuteSV\" id=\"link-25187\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cuteSV<\/a>\n<!-- Time to render name section of link id 25187: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Long read based human genomic structural variation detection with cuteSV.<\/p>\n<!-- Time to render link large description section of link id 25187: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cuteSV> How to use <\/a>\n<!-- Time to render notes section of link id 25187: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25187: 0.00020718574523926 --> \n<tr><td><a href=\"https:\/\/github.com\/MartinPippel\/DAmar\" id=\"link-24191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAmar<\/a>\n<!-- Time to render name section of link id 24191: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Long read QC, assembly and scaffolding pipeline for PacBio or Oxford Nanopore long-read sequencing data. T he pipeline produces a number of QC metrics at various stages as well as incorporating further technologies including Bionano, 10x and HiC data to scaffold the created contigs. DAmar, is a hybrid of the earlier Marvel, Dazzler, and Daccord systems of the Eugene Myers lab.<\/p>\n<!-- Time to render link large description section of link id 24191: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24191: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24191: 0.00021791458129883 --> \n<tr><td><a href=\"https:\/\/github.com\/thegenemyers\/DAZZ_DB\" id=\"link-23614\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAZZ_DB<\/a>\n<!-- Time to render name section of link id 23614: 4.0531158447266E-6 --> \n<\/td>\n<td><p>To facilitate the multiple phases of the dazzler assembler, we organize all the read data into what is effectively a \"database\" of the reads and their meta-information.<\/p>\n<!-- Time to render link large description section of link id 23614: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23614: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23614: 0.00020813941955566 --> \n<tr><td><a href=\"https:\/\/github.com\/yechengxi\/DBG2OLC\" id=\"link-24047\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DBG2OLC<\/a>\n<!-- Time to render name section of link id 24047: 3.814697265625E-6 --> \n<\/td>\n<td><p>The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24047: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24047: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24047: 0.00020885467529297 --> \n<tr><td><a href=\"https:\/\/github.com\/LuoGroup2023\/DeChat\" id=\"link-25400\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeChat<\/a>\n<!-- Time to render name section of link id 25400: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.<\/p>\n<!-- Time to render link large description section of link id 25400: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DeChat> How to use <\/a>\n<!-- Time to render notes section of link id 25400: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25400: 0.00020599365234375 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Deepbinner\" id=\"link-24010\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Deepbinner<\/a>\n<!-- Time to render name section of link id 24010: 6.1988830566406E-6 --> \n<\/td>\n<td><p>Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porechop), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads.<\/p>\n<!-- Time to render link large description section of link id 24010: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24010: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24010: 0.00020909309387207 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfomaticsCSU\/deepsignal\" id=\"link-24197\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepSignal<\/a>\n<!-- Time to render name section of link id 24197: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Detecting methylation using signal-level features from Nanopore sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24197: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24197: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24197: 0.00021910667419434 --> \n<tr><td><a href=\"https:\/\/github.com\/a-ludi\/dentist\" id=\"link-24198\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DENTIST<\/a>\n<!-- Time to render name section of link id 24198: 1.9073486328125E-6 --> \n<\/td>\n<td><p>DENTIST is a sensitive, highly-accurate and automated pipeline method to close gaps in (short read) assemblies with long reads.<\/p>\n<!-- Time to render link large description section of link id 24198: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24198: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24198: 0.00012803077697754 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/FABuLOUS\" id=\"link-24222\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FABuLOUS<\/a>\n<!-- Time to render name section of link id 24222: 1.4066696166992E-5 --> \n<\/td>\n<td><p>A gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly. Initially called TGS-GapCloser.<\/p>\n<!-- Time to render link large description section of link id 24222: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24222: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24222: 0.00012087821960449 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/falcon\" id=\"link-23622\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON<\/a>\n<!-- Time to render name section of link id 23622: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Falcon: a set of tools for fast aligning long reads for consensus and assembly<\/p>\n<!-- Time to render link large description section of link id 23622: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23622: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23622: 9.1075897216797E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/phasegenomics\/FALCON-Phase\" id=\"link-24038\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FALCON-Phase<\/a>\n<!-- Time to render name section of link id 24038: 2.1457672119141E-6 --> \n<\/td>\n<td><p>FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds.<\/p>\n<!-- Time to render link large description section of link id 24038: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24038: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24038: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/OpenGene\/fastplong\" id=\"link-25596\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastplong<\/a>\n<!-- Time to render name section of link id 25596: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ultra-fast preprocessing and quality control for long-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25596: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastplong> How to use <\/a>\n<!-- Time to render notes section of link id 25596: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25596: 0.00010108947753906 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Filtlong\" id=\"link-24232\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Filtlong<\/a>\n<!-- Time to render name section of link id 24232: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Filtlong is a tool for filtering long reads by quality.<\/p>\n<!-- Time to render link large description section of link id 24232: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Filtlong> How to use <\/a>\n<!-- Time to render notes section of link id 24232: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24232: 9.5129013061523E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/BrooksLabUCSC\/flair\" id=\"link-24236\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAIR<\/a>\n<!-- Time to render name section of link id 24236: 2.1457672119141E-6 --> \n<\/td>\n<td><p>FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24236: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24236: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24236: 9.4890594482422E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/baoe\/FLAS\" id=\"link-24096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAS<\/a>\n<!-- Time to render name section of link id 24096: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FLAS is software that makes self-correction for PacBio long reads with fast speed and high throughput.<\/p>\n<!-- Time to render link large description section of link id 24096: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24096: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24096: 9.608268737793E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/fenderglass\/Flye\" id=\"link-24015\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Flye<\/a>\n<!-- Time to render name section of link id 24015: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.<\/p>\n<!-- Time to render link large description section of link id 24015: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Flye> How to use <\/a>\n<!-- Time to render notes section of link id 24015: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24015: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/holtjma\/fmlrc\" id=\"link-24237\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FMLRC<\/a>\n<!-- Time to render name section of link id 24237: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24237: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24237: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24237: 9.608268737793E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/jwanglab\/fmlrc2\" id=\"link-25112\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FMLRC2<\/a>\n<!-- Time to render name section of link id 25112: 1.7881393432617E-5 --> \n<\/td>\n<td><p>FMLRC2 performs error correction\/polishing of long erroneous sequences with accurate short reads. As such, it can be used as\u00a0<em>both<\/em>\u00a0an error-correction tool <<a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2051-3\" rel=\"nofollow\">1<\/a>> for raw long reads (ex. Oxford Nanopore)\u00a0<em>and<\/em>\u00a0a polishing tool <<a href=\"http:\/\/biorxiv.org\/content\/early\/2022\/07\/23\/2022.07.22.501182\" rel=\"nofollow\">2<\/a>> for\u00a0<em>de novo<\/em>\u00a0assemblies.<\/p>\n<!-- Time to render link large description section of link id 25112: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FMLRC2> How to use <\/a>\n<!-- Time to render notes section of link id 25112: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25112: 0.00015091896057129 --> \n<tr><td><a href=\"https:\/\/github.com\/yeeus\/GCI.git\" id=\"link-25561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GCI<\/a>\n<!-- Time to render name section of link id 25561: 1.9073486328125E-6 --> \n<\/td>\n<td>Genome Continuity Inspector (GCI) is an assembly assessment tool for high-quality genomes (e.g. T2T genomes), in base resolution.\n<!-- Time to render link large description section of link id 25561: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCI> How to use <\/a>\n<!-- Time to render notes section of link id 25561: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25561: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/maickrau\/GraphAligner\" id=\"link-24261\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphAligner<\/a>\n<!-- Time to render name section of link id 24261: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Seed-and-extend program for aligning long error-prone reads to genome graphs.<\/p>\n<!-- Time to render link large description section of link id 24261: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GraphAligner> How to use <\/a>\n<!-- Time to render notes section of link id 24261: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24261: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/isovic\/graphmap\" id=\"link-24262\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphMap<\/a>\n<!-- Time to render name section of link id 24262: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A highly sensitive and accurate mapper for long, error-prone reads.<\/p>\n<!-- Time to render link large description section of link id 24262: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24262: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24262: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/rolandfaure\/hairsplitter\" id=\"link-26093\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hairsplitter<\/a>\n<!-- Time to render name section of link id 26093: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.<\/p>\n<!-- Time to render link large description section of link id 26093: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hairsplitter> How to use <\/a>\n<!-- Time to render notes section of link id 26093: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26093: 0.0001380443572998 --> \n<tr><td><a href=\"https:\/\/github.com\/smajidian\/Hap10\" id=\"link-24270\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hap10<\/a>\n<!-- Time to render name section of link id 24270: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The goal is to reconstruct accurate and long haplotypes polyploid genome using linked reads.<\/p>\n<!-- Time to render link large description section of link id 24270: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24270: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24270: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/institut-de-genomique\/HAPO-G\" id=\"link-24274\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Hapo-G<\/a>\n<!-- Time to render name section of link id 24274: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.<\/p>\n<!-- Time to render link large description section of link id 24274: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Hapo-G> How to use <\/a>\n<!-- Time to render notes section of link id 24274: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24274: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/vpc-ccg\/haslr\" id=\"link-24275\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HASLR<\/a>\n<!-- Time to render name section of link id 24275: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.<\/p>\n<!-- Time to render link large description section of link id 24275: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24275: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24275: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/NDBL\/HECIL\" id=\"link-24033\" class=\"track_this_link \" rel=\"noopener noreferrer\">HECIL<\/a>\n<!-- Time to render name section of link id 24033: 9.5367431640625E-7 --> \n<\/td>\n<td><p>Hybrid Error Correction of Long Reads using Iterative Learning<\/p>\n<!-- Time to render link large description section of link id 24033: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24033: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24033: 9.2029571533203E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/kishwarshafin\/helen\" id=\"link-24284\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HELEN<\/a>\n<!-- Time to render name section of link id 24284: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HELEN (Homopolymer Encoded Long-read Error-corrector for Nanopore) uses a Recurrent-Neural-Network (RNN) based Multi-Task Learning (MTL) model that can predict a base and a run-length for each genomic position using the weights generated by MarginPolish. This installation includes MarginPolish.<\/p>\n<!-- Time to render link large description section of link id 24284: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24284: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24284: 9.1075897216797E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/HG-CoLoR\" id=\"link-24044\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HG-CoLoR<\/a>\n<!-- Time to render name section of link id 24044: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HG-CoLoR (Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads) is a hybrid method for the error correction of long reads that both aligns the short reads to the long reads, and uses a variable-order de Bruijn graph, in a seed-and-extend approach.<\/p>\n<!-- Time to render link large description section of link id 24044: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24044: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24044: 9.608268737793E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/sheinasim\/HiFiAdapterFilt\" id=\"link-24291\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HiFiAdapterFilt<\/a>\n<!-- Time to render name section of link id 24291: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences.<\/p>\n<!-- Time to render link large description section of link id 24291: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiFiAdapterFilt> How to use <\/a>\n<!-- Time to render notes section of link id 24291: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24291: 0.00010490417480469 --> \n<tr><td><a href=\"https:\/\/github.com\/chhylp123\/hifiasm\" id=\"link-24292\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\">hifiasm<\/a>\n<!-- Time to render name section of link id 24292: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome.<\/p>\n<!-- Time to render link large description section of link id 24292: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hifiasm> How to use <\/a>\n<!-- Time to render notes section of link id 24292: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24292: 9.0837478637695E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/xfengnefx\/hifiasm-meta\" id=\"link-24293\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\">hifiasm-meta<\/a>\n<!-- Time to render name section of link id 24293: 1.9073486328125E-6 --> \n<\/td>\n<td><p>De novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.<\/p>\n<!-- Time to render link large description section of link id 24293: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hifiasm-meta> How to use <\/a>\n<!-- Time to render notes section of link id 24293: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24293: 8.9883804321289E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbbioconda\/wiki\/Improved-Phased-Assembler\" id=\"link-24323\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IPA<\/a>\n<!-- Time to render name section of link id 24323: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly.<\/p>\n<!-- Time to render link large description section of link id 24323: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IPA> How to use <\/a>\n<!-- Time to render notes section of link id 24323: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24323: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/IsoSeq\" id=\"link-24328\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IsoSeq<\/a>\n<!-- Time to render name section of link id 24328: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads.<\/p>\n<!-- Time to render link large description section of link id 24328: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IsoSeq> How to use <\/a>\n<!-- Time to render notes section of link id 24328: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24328: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/biointec\/jabba\" id=\"link-24329\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jabba<\/a>\n<!-- Time to render name section of link id 24329: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A hybrid error correction tool for sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24329: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24329: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24329: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/mcfrith\/lamassemble\" id=\"link-24341\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lamassemble<\/a>\n<!-- Time to render name section of link id 24341: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Merge overlapping \"long\" DNA reads into a consensus sequence.<\/p>\n<!-- Time to render link large description section of link id 24341: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24341: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24341: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/pacificbiosciences\/barcoding\/\" id=\"link-24347\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lima<\/a>\n<!-- Time to render name section of link id 24347: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Demultiplex Barcoded PacBio Samples.<\/p>\n<!-- Time to render link large description section of link id 24347: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24347: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24347: 9.608268737793E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/rwtourdot\/linker\" id=\"link-24348\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Linker<\/a>\n<!-- Time to render name section of link id 24348: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Linker is a suite of C++ tools useful for interpreting long and linked read sequencing of cancer genomes.<\/p>\n<!-- Time to render link large description section of link id 24348: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24348: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24348: 9.3936920166016E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/WGLab\/LIQA\" id=\"link-24349\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LIQA<\/a>\n<!-- Time to render name section of link id 24349: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Long-read Isoform Quantification and Analysis) is an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data.<\/p>\n<!-- Time to render link large description section of link id 24349: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24349: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24349: 9.7036361694336E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/yfukasawa\/LongQC\" id=\"link-24354\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LongQC<\/a>\n<!-- Time to render name section of link id 24354: 1.9073486328125E-6 --> \n<\/td>\n<td><p>LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc.<\/p>\n<!-- Time to render link large description section of link id 24354: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LongQC> How to use <\/a>\n<!-- Time to render notes section of link id 24354: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24354: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/pjedge\/longshot\" id=\"link-24355\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">longshot<\/a>\n<!-- Time to render name section of link id 24355: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).<\/p>\n<!-- Time to render link large description section of link id 24355: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24355: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24355: 9.5844268798828E-5 --> \n<tr><td><a href=\"http:\/\/atgc.lirmm.fr\/lordec\/\" id=\"link-23657\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LoRDEC<\/a>\n<!-- Time to render name section of link id 23657: 9.5367431640625E-7 --> \n<\/td>\n<td><p>LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.<\/p>\n<!-- Time to render link large description section of link id 23657: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LoRDEC> How to use <\/a>\n<!-- Time to render notes section of link id 23657: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23657: 9.608268737793E-5 --> \n<tr><td><a href=\"http:\/\/www.fishbrowser.org\/software\/LR_Gapcloser\/index.php\/Home\/Index\/Index.html\" id=\"link-24030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LR_Gapcloser<\/a>\n<!-- Time to render name section of link id 24030: 2.1457672119141E-6 --> \n<\/td>\n<td><p>\u00a0LR_Gapcloser is a gap closing tool using uncorrected or corrected long reads generated from Pacbio platform or Nanopore platform.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24030: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24030: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24030: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/shingocat\/lrscaf\" id=\"link-23977\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LRScaf<\/a>\n<!-- Time to render name section of link id 23977: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TGS scaffolding . Improving draft genomes using long noisy reads.<\/p>\n<!-- Time to render link large description section of link id 23977: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23977: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23977: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/schloi\/MARVEL\" id=\"link-23888\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MARVEL<\/a>\n<!-- Time to render name section of link id 23888: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.<\/p>\n<!-- Time to render link large description section of link id 23888: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23888: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23888: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/MashMap\" id=\"link-24367\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MashMap<\/a>\n<!-- Time to render name section of link id 24367: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. \u00a0It can be useful for mapping genome assembly or long reads (PacBio\/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, Mashmap computes alignment boundaries and identity estimates using\u00a0k-mers. It does not compute the alignments explicitly, but rather estimates a\u00a0k-mer based\u00a0Jaccard similarity\u00a0using a combination of\u00a0Minimizers\u00a0and\u00a0MinHash. This is then converted to an estimate of sequence identity using the\u00a0Mash distance.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24367: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24367: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24367: 0.00013518333435059 --> \n<tr><td><a href=\"http:\/\/www.genome.umd.edu\/masurca.html\" id=\"link-23661\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MaSuRCA<\/a>\n<!-- Time to render name section of link id 23661: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MaSuRCA is whole genome assembly software. It combines the efficiency of the de\u00a0Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454)<\/p>\n<!-- Time to render link large description section of link id 23661: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MaSuRCA> How to use <\/a>\n<!-- Time to render notes section of link id 23661: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23661: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/al-mcintyre\/mCaller\" id=\"link-24063\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mCaller<\/a>\n<!-- Time to render name section of link id 24063: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This program is designed to call m6A from nanopore data using the differences between measured and expected currents.<\/p>\n<!-- Time to render link large description section of link id 24063: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24063: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24063: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/megalodon\" id=\"link-24129\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Megalodon<\/a>\n<!-- Time to render name section of link id 24129: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Megalodon provides \"basecalling augmentation\" for raw nanopore sequencing reads, including direct, reference-guided SNP and modified base calling.<\/p>\n<!-- Time to render link large description section of link id 24129: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24129: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24129: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/LANL-Bioinformatics\/MeGAMerge\" id=\"link-23925\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MeGAMerge<\/a>\n<!-- Time to render name section of link id 23925: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool to merge assembled contigs, long reads from metagenomic sequencing runs<\/p>\n<!-- Time to render link large description section of link id 23925: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23925: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23925: 9.8228454589844E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/DiltheyLab\/MetaMaps\" id=\"link-23971\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaMaps<\/a>\n<!-- Time to render name section of link id 23971: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MetaMaps is tool specifically developed for the analysis of long-read (PacBio\/ONT) metagenomic datasets. It simultaenously carries out read assignment and sample composition estimation. It is faster than classical exact alignment-based approaches, and its output is more information-rich than that of kmer-spectra-based methods. For example, each MetaMaps alignment comes with an approximate alignment location, an estimated alignment identity and a mapping quality.<\/p>\n<!-- Time to render link large description section of link id 23971: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23971: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23971: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/miniasm\" id=\"link-23810\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniasm<\/a>\n<!-- Time to render name section of link id 23810: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ultrafast de novo assembly for long noisy reads (though having no consensus step).<\/p>\n<!-- Time to render link large description section of link id 23810: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniasm> How to use <\/a>\n<!-- Time to render notes section of link id 23810: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23810: 0.00012707710266113 --> \n<tr><td><a href=\"https:\/\/github.com\/calacademy-research\/minibar\" id=\"link-25619\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">minibar<\/a>\n<!-- Time to render name section of link id 25619: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Dual barcode and primer demultiplexing for MinION sequenced reads.<\/p>\n<!-- Time to render link large description section of link id 25619: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_minibar> How to use <\/a>\n<!-- Time to render notes section of link id 25619: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25619: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/roblanf\/minion_qc\" id=\"link-24383\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MinIONQC<\/a>\n<!-- Time to render name section of link id 24383: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast and effective quality control for MinION and PromethION sequencing data<\/p>\n<!-- Time to render link large description section of link id 24383: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24383: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24383: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Minipolish\" id=\"link-24384\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minipolish<\/a>\n<!-- Time to render name section of link id 24384: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for Racon polishing of miniasm assemblies.<\/p>\n<!-- Time to render link large description section of link id 24384: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minipolish> How to use <\/a>\n<!-- Time to render notes section of link id 24384: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24384: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/berkeleylab\/jgi-miniscrub\/src\/master\/\" id=\"link-24386\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiniScrub<\/a>\n<!-- Time to render name section of link id 24386: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MiniScrub is a de novo long sequencing read preprocessing method that improves read quality by predicting and removing (\"scrubbing\") read segments that have a high concentration of errors.<\/p>\n<!-- Time to render link large description section of link id 24386: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24386: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24386: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/epi2me-labs\/modbam2bed\" id=\"link-24714\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">modbam2bed<\/a>\n<!-- Time to render name section of link id 24714: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.<\/p>\n<!-- Time to render link large description section of link id 24714: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_modbam2bed> How to use <\/a>\n<!-- Time to render notes section of link id 24714: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24714: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/WGLab\/NanoCaller\" id=\"link-24406\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCaller<\/a>\n<!-- Time to render name section of link id 24406: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs\/indels from long-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24406: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoCaller> How to use <\/a>\n<!-- Time to render notes section of link id 24406: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24406: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoComp\" id=\"link-23942\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoComp<\/a>\n<!-- Time to render name section of link id 23942: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Compare multiple runs of long read sequencing data and alignments.<\/p>\n<!-- Time to render link large description section of link id 23942: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.11.1\n<!-- Time to render notes section of link id 23942: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23942: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/CarlierLab\/NanoSeq\" id=\"link-25615\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoSeq<\/a>\n<!-- Time to render name section of link id 25615: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Pipeline used at the LIPME to assemble plasmid and PCR sequences with Nanopore.<\/p>\n<!-- Time to render link large description section of link id 25615: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoSeq> How to use <\/a>\n<!-- Time to render notes section of link id 25615: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25615: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/NanoSim\" id=\"link-24029\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoSim<\/a>\n<!-- Time to render name section of link id 24029: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology.<\/p>\n<!-- Time to render link large description section of link id 24029: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoSim> How to use <\/a>\n<!-- Time to render notes section of link id 24029: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24029: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/nanospc.mmmoxford.uk\" id=\"link-24409\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoSPC<\/a>\n<!-- Time to render name section of link id 24409: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NanoSPC is a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24409: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoSPC> How to use <\/a>\n<!-- Time to render notes section of link id 24409: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24409: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.genoscope.cns.fr\/externe\/nas\/\" id=\"link-23990\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NaS<\/a>\n<!-- Time to render name section of link id 23990: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NaS is a hybrid approach developed to take advantage of data generated using MinION device. It combines Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads<\/p>\n<!-- Time to render link large description section of link id 23990: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23990: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23990: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/NECAT\" id=\"link-24411\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NECAT<\/a>\n<!-- Time to render name section of link id 24411: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.<\/p>\n<!-- Time to render link large description section of link id 24411: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NECAT> How to use <\/a>\n<!-- Time to render notes section of link id 24411: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24411: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/Nextomics\/NextDenovo\" id=\"link-24414\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NextDenovo<\/a>\n<!-- Time to render name section of link id 24414: 2.8610229492188E-6 --> \n<\/td>\n<td><p>NextDenovo is a string graph-based de novo assembler for TGS long reads.<\/p>\n<!-- Time to render link large description section of link id 24414: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextDenovo> How to use <\/a>\n<!-- Time to render notes section of link id 24414: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24414: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/philres\/ngmlr\" id=\"link-24037\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NGMLR<\/a>\n<!-- Time to render name section of link id 24037: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations SV detection from paired end reads mapping<\/p>\n<!-- Time to render link large description section of link id 24037: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NGMLR> How to use <\/a>\n<!-- Time to render notes section of link id 24037: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24037: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/ndierckx\/NOVOLoci\" id=\"link-26077\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NOVOLoci<\/a>\n<!-- Time to render name section of link id 26077: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NOVOLoci is a haplotype aware assembler for targeted assembly or whole genome assembly of small genomes.\u00a0<\/p>\r\n<p dir=\"auto\">We currently recommend limiting the assembly size to regions &lt;20 Mb in targeted-mode and diploid genomes that are &lt;250 Mb in WG-mode, with a minimum sequencing depth of 10x per haplotype.<\/p>\r\n<p dir=\"auto\">If you do need to phase accuratly and you have HiFi or R10 ONT data, it is adviced to use Hifiasm, as it is has a much shorter runtime.<\/p>\r\n<p>Currently it is only available for Nanopore, PacBio and hybrid options will be available soon.<\/p>\n<!-- Time to render link large description section of link id 26077: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NOVOLoci> How to use <\/a>\n<!-- Time to render notes section of link id 26077: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26077: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/dzerbino\/oases\" id=\"link-23683\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Oases<\/a>\n<!-- Time to render name section of link id 23683: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz). <br \/>\r\n<br \/>\r\nOases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.<\/p>\n<!-- Time to render link large description section of link id 23683: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Oases> How to use <\/a>\n<!-- Time to render notes section of link id 23683: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23683: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/c-zhou\/oatk\" id=\"link-25662\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">oatk<\/a>\n<!-- Time to render name section of link id 25662: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A organelle de novo genome assembly toolkit. (Install include OatkDB)<\/p>\n<!-- Time to render link large description section of link id 25662: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Oatk> How to use <\/a>\n<!-- Time to render notes section of link id 25662: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25662: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/ont_fast5_api\" id=\"link-24086\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ont_fast5_api<\/a>\n<!-- Time to render name section of link id 24086: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore fast5 file format.<\/p>\n<!-- Time to render link large description section of link id 24086: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ont_fast5_api> How to use <\/a>\n<!-- Time to render notes section of link id 24086: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24086: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/aubombarely\/Organelle_PBA\" id=\"link-24429\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Organelle_PBA<\/a>\n<!-- Time to render name section of link id 24429: 1.9073486328125E-6 --> \n<\/td>\n<td><p>OrganelleRef_PBA is a script to perform a de-novo PacBio assemblies of any organelle (chloroplast or mitochondrial genomes) using several programs.<\/p>\n<!-- Time to render link large description section of link id 24429: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24429: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24429: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/swarris\/Pacasus\" id=\"link-24006\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pacasus<\/a>\n<!-- Time to render name section of link id 24006: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tool for detecting and cleaning PacBio \/ Nanopore long reads after whole genome amplification.<\/p>\n<!-- Time to render link large description section of link id 24006: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24006: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24006: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbmm2\" id=\"link-25904\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pbmm2<\/a>\n<!-- Time to render name section of link id 25904: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A minimap2 frontend for PacBio native data format.<\/p>\n<!-- Time to render link large description section of link id 25904: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pbmm2> How to use <\/a>\n<!-- Time to render notes section of link id 25904: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25904: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/cschin\/peregrine-2021\" id=\"link-24093\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Peregrine<\/a>\n<!-- Time to render name section of link id 24093: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Peregrine is a fast genome assembler for accurate long reads (length &gt; 10kb, accuraccy &gt; 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus.<\/p>\n<!-- Time to render link large description section of link id 24093: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Peregrine> How to use <\/a>\n<!-- Time to render notes section of link id 24093: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24093: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/nanoporetech.github.io\/pomoxis\/index.html\" id=\"link-24458\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pomoxis<\/a>\n<!-- Time to render name section of link id 24458: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing.<\/p>\n<!-- Time to render link large description section of link id 24458: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24458: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24458: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bonsai-team\/Porechop_ABI\" id=\"link-24099\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Porechop_ABI<\/a>\n<!-- Time to render name section of link id 24099: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Porechop_abi (ab initio) is an extension of Porechop that is able to infer the adapter sequence from the Oxford Nanopore reads. It discovers the adapter sequence from the reads using approximate k-mers and assembly, and add the sequence found to the adapter list (adapters.py file).<\/p>\n<!-- Time to render link large description section of link id 24099: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Porechop_ABI> How to use <\/a>\n<!-- Time to render notes section of link id 24099: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24099: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/epi2me-labs\/pychopper\" id=\"link-25702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pychopper<\/a>\n<!-- Time to render name section of link id 25702: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.<\/p>\n<!-- Time to render link large description section of link id 25702: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pychopper> How to use <\/a>\n<!-- Time to render notes section of link id 25702: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25702: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/a-slide\/pycoQC\" id=\"link-24034\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pycoQC<\/a>\n<!-- Time to render name section of link id 24034: 2.1457672119141E-6 --> \n<\/td>\n<td><p>pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore\/Guppy)<\/p>\n<!-- Time to render link large description section of link id 24034: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pycoQC> How to use <\/a>\n<!-- Time to render notes section of link id 24034: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24034: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Rebaler\" id=\"link-24478\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Rabaler<\/a>\n<!-- Time to render name section of link id 24478: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences.<\/p>\n<!-- Time to render link large description section of link id 24478: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24478: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24478: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/lbcb-sci\/racon\" id=\"link-23828\" class=\"track_this_link \" rel=\"noopener noreferrer\">Racon<\/a>\n<!-- Time to render name section of link id 23828: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Consensus module for raw de novo DNA assembly of long uncorrected reads.<\/p>\n<!-- Time to render link large description section of link id 23828: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Racon> How to use <\/a>\n<!-- Time to render notes section of link id 23828: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23828: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/at-cg\/RAFT\" id=\"link-25101\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAFT<\/a>\n<!-- Time to render name section of link id 25101: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RAFT (Repeat Aware Fragmentation Tool) is an algorithm designed to improve assembly quality by rescuing contained reads.<\/p>\r\n<p dir=\"auto\">RAFT breaks long reads into smaller sub-reads by following an algorithm described in our <a href=\"https:\/\/github.com\/at-cg\/RAFT#papers\">preprint<\/a>. The read fragmentation allows an OLC assembler to retain contained reads during string graph construction. When input reads have non-uniform lengths, retaining contained reads improves assembly contiguity and base-level accuracy. The inputs to RAFT include an error-corrected read file in FASTA\/FASTQ format and an all-vs-all alignment file in PAF format. It performs read fragmentation and outputs the fragmented reads in FASTA format.<\/p>\r\n<p dir=\"auto\">We recommend users to use\u00a0<a href=\"https:\/\/github.com\/chhylp123\/hifiasm\">hifiasm<\/a>\u00a0for the initial steps (read error correction, all-vs-all overlap computation) and also for the final step (assembly of fragmented reads). The assembly output format of hifiasm is described\u00a0<a href=\"https:\/\/hifiasm.readthedocs.io\/en\/latest\/interpreting-output.html#interpreting-output\" rel=\"nofollow\">here<\/a>.<\/p>\r\n<p dir=\"auto\"><em>The RAFT-hifiasm workflow is recommended for long accurate reads with non-uniform length distribution (e.g., ONT Duplex, or a mixture of ONT Duplex and HiFi reads). ONT UL reads can optionally be\u00a0<a href=\"https:\/\/github.com\/chhylp123\/hifiasm#ul\">integrated<\/a>\u00a0during the final assembly step.<\/em><\/p>\n<!-- Time to render link large description section of link id 25101: 1.1920928955078E-6 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAFT> How to use <\/a>\n<!-- Time to render notes section of link id 25101: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25101: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/Ratatosk\" id=\"link-24485\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ratatosk<\/a>\n<!-- Time to render name section of link id 24485: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Ratatosk is a phased error correction tool for erroneous long reads based on compacted and colored de Bruijn graphs built from accurate short reads.<\/p>\n<!-- Time to render link large description section of link id 24485: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24485: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24485: 0.00012087821960449 --> \n<tr><td><a href=\"https:\/\/github.com\/ekimb\/rust-mdbg\" id=\"link-24506\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">rust-mdbg<\/a>\n<!-- Time to render name section of link id 24506: 2.8610229492188E-6 --> \n<\/td>\n<td><p>rust-mdbg is an ultra-fast minimizer-space de Bruijn graph (mdBG) implementation, geared towards the assembly of long and accurate reads such as PacBio HiFi.<\/p>\n<!-- Time to render link large description section of link id 24506: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rust-mdbg> How to use <\/a>\n<!-- Time to render notes section of link id 24506: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24506: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/paoloshasta\/shasta\" id=\"link-24118\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Shasta<\/a>\n<!-- Time to render name section of link id 24118: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.<\/p>\n<!-- Time to render link large description section of link id 24118: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Shasta> How to use <\/a>\n<!-- Time to render notes section of link id 24118: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24118: 0.00012993812561035 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/SLR-superscaffolder\" id=\"link-24521\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLR-superscaffolder<\/a>\n<!-- Time to render name section of link id 24521: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is a scaffold assembler designed for stLFR reads. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds.<\/p>\n<!-- Time to render link large description section of link id 24521: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24521: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24521: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/spliced_bam2gff\" id=\"link-24605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spliced_bam2gff<\/a>\n<!-- Time to render name section of link id 24605: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool to convert spliced BAM alignments into GFF2 format.<\/p>\n<!-- Time to render link large description section of link id 24605: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24605: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24605: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/ConesaLab\/SQANTI3\" id=\"link-24537\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SQANTI3<\/a>\n<!-- Time to render name section of link id 24537: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SQANTI3 is the newest version of the SQANTI tool (publication) that merges features from SQANTI, (code repository) and SQANTI2 (code repository), together with new additions. SQANTI3 will continue as an integrated development aiming to providing you the best characterization possible for your new long read-defined transcriptome. SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, that also includes IsoAnnot and tappAS.<\/p>\n<!-- Time to render link large description section of link id 24537: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24537: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24537: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/Psy-Fer\/SquiggleKit\" id=\"link-24127\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SquiggleKit<\/a>\n<!-- Time to render name section of link id 24127: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A toolkit for manipulating nanopore signal data.<\/p>\n<!-- Time to render link large description section of link id 24127: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24127: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24127: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.baseclear.com\/genomics\/bioinformatics\/basetools\/SSPACE_longread\" id=\"link-23738\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SSPACE-LongRead<\/a>\n<!-- Time to render name section of link id 23738: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads).<\/p>\n<!-- Time to render link large description section of link id 23738: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23738: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23738: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/marcpaga\/sturgeon\" id=\"link-25424\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sturgeon<\/a>\n<!-- Time to render name section of link id 25424: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Sturgeon is a CNS neural network classifier for tumour classification<\/p>\n<!-- Time to render link large description section of link id 25424: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sturgeon> How to use <\/a>\n<!-- Time to render notes section of link id 25424: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25424: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/eldariont\/svim\" id=\"link-24103\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVIM<\/a>\n<!-- Time to render name section of link id 24103: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SVIM is a structural variant caller for long reads. It is able to detect, classify and genotype five different classes of structural variants.<\/p>\n<!-- Time to render link large description section of link id 24103: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVIM> How to use <\/a>\n<!-- Time to render notes section of link id 24103: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24103: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/llecompte\/SVJedi\" id=\"link-24552\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi<\/a>\n<!-- Time to render name section of link id 24552: 2.8610229492188E-6 --> \n<\/td>\n<td><p>SVJedi is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24552: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24552: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24552: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/SandraLouise\/SVJedi-graph\" id=\"link-24752\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi-graph<\/a>\n<!-- Time to render name section of link id 24752: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SVJedi-graph is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24752: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVJedi-graph> How to use <\/a>\n<!-- Time to render notes section of link id 24752: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24752: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/johnomics\/tapestry\" id=\"link-24094\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tapestry<\/a>\n<!-- Time to render name section of link id 24094: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tapestry is a tool to validate and edit small eukaryotic genome assemblies using long sequence reads. It is designed to help identify complete chromosomes, symbionts, haplotypes, complex features and errors in close-to-complete genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24094: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24094: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24094: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/BGI-Qingdao\/TGSGapFiller\" id=\"link-24562\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TGSGapFiller<\/a>\n<!-- Time to render name section of link id 24562: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A gap filling tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.<\/p>\n<!-- Time to render link large description section of link id 24562: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24562: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24562: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/tombo\" id=\"link-24011\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tombo<\/a>\n<!-- Time to render name section of link id 24011: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24011: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24011: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24011: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Trycycler\" id=\"link-24571\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trycycler<\/a>\n<!-- Time to render name section of link id 24571: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 24571: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Trycycler> How to use <\/a>\n<!-- Time to render notes section of link id 24571: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24571: 0.00011920928955078 --> \n<tr><td><a href=\"https:\/\/github.com\/ksahlin\/ultra\" id=\"link-24322\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">uLTRA<\/a>\n<!-- Time to render name section of link id 24322: 1.9073486328125E-6 --> \n<\/td>\n<td><p>uLTRA is a tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations.<\/p>\n<!-- Time to render link large description section of link id 24322: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_uLTRA> How to use <\/a>\n<!-- Time to render notes section of link id 24322: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24322: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/HaploKit\/vechat\" id=\"link-24910\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VeChat<\/a>\n<!-- Time to render name section of link id 24910: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Correcting errors in noisy long reads using variation graphs.<\/p>\n<!-- Time to render link large description section of link id 24910: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VeChat> How to use <\/a>\n<!-- Time to render notes section of link id 24910: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24910: 0.00019216537475586 --> \n<tr><td><a href=\"https:\/\/github.com\/dzerbino\/velvet\" id=\"link-23761\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Velvet<\/a>\n<!-- Time to render name section of link id 23761: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. <br \/>\r\n<br \/>\r\nVelvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.<\/p>\n<!-- Time to render link large description section of link id 23761: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Velvet> How to use <\/a>\n<!-- Time to render notes section of link id 23761: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23761: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/sverre-phd-work\/voyager\/src\/master\/\" id=\"link-25922\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Voyager<\/a>\n<!-- Time to render name section of link id 25922: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Rapid and efficient mapping algorithm for long sequencing reads with insertion- and deletion errors. Mapping long reads in Sorted Motif Distance Space.<\/p>\n<!-- Time to render link large description section of link id 25922: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Voyager> How to use <\/a>\n<!-- Time to render notes section of link id 25922: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25922: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/whatshap\/whatshap\/\" id=\"link-24592\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WhatsHap<\/a>\n<!-- Time to render name section of link id 24592: 1.9073486328125E-6 --> \n<\/td>\n<td><p>WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.<\/p>\n<!-- Time to render link large description section of link id 24592: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WhatsHap> How to use <\/a>\n<!-- Time to render notes section of link id 24592: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24592: 0.00012612342834473 --> \n<tr><td><a href=\"https:\/\/github.com\/natir\/yacrd\" id=\"link-24100\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">yacrd<\/a>\n<!-- Time to render name section of link id 24100: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Yet Another Chimeric Read Detector for long reads<\/p>\n<!-- Time to render link large description section of link id 24100: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24100: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24100: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/yak\" id=\"link-24598\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Yak<\/a>\n<!-- Time to render name section of link id 24598: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Yak is initially developed for two specific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads.<\/p>\n<!-- Time to render link large description section of link id 24598: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24598: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24598: 9.8943710327148E-5 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link 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class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/beagle-dev\/beagle-lib\" id=\"link-24016\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle-lib<\/a>\n<!-- Time to render name section of link id 24016: 2.8610229492188E-6 --> \n<\/td>\n<td><p>BEAGLE-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages<\/p>\n<!-- Time to render link large description section of link id 24016: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Beagle-lib> How to use <\/a>\n<!-- Time to render notes section of link id 24016: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24016: 0.00012898445129395 --> \n<tr><td><a href=\"http:\/\/meta.usc.edu\/softs\/lsa\/\" id=\"link-24013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eLSA<\/a>\n<!-- Time to render name section of link id 24013: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Extended Local Similarity Analysis -- Finding Time-Dependent Associations in Time Series Datasets<\/p>\n<!-- Time to render link large description section of link id 24013: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24013: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24013: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/GenoML\/genoml2\" id=\"link-25757\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenoML2<\/a>\n<!-- Time to render name section of link id 25757: 3.0994415283203E-6 --> \n<\/td>\n<td><p>GenoML (genoml2) is an open source Python package. It is an automated machine learning (autoML) platform for genomics data.<\/p>\n<!-- Time to render link large description section of link id 25757: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenoML2> How to use <\/a>\n<!-- Time to render notes section of link id 25757: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25757: 0.00044488906860352 --> \n<tr><td><a href=\"http:\/\/www.gromacs.org\/About_Gromacs\" id=\"link-23876\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GROMACS<\/a>\n<!-- Time to render name section of link id 23876: 6.9141387939453E-6 --> \n<\/td>\n<td><p>GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.<\/p>\n<!-- Time to render link large description section of link id 23876: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GROMACS> How to use <\/a>\n<!-- Time to render notes section of link id 23876: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23876: 0.00035905838012695 --> \n<tr><td><a href=\"http:\/\/mcmc-jags.sourceforge.net\" id=\"link-24330\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JAGS<\/a>\n<!-- Time to render name section of link id 24330: 6.9141387939453E-6 --> \n<\/td>\n<td><p>JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.<\/p>\n<!-- Time to render link large description section of link id 24330: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_JAGS> How to use <\/a>\n<!-- Time to render notes section of link id 24330: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24330: 0.00035810470581055 --> \n<tr><td><a href=\"https:\/\/micans.org\/mcl\/\" id=\"link-23919\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MCL<\/a>\n<!-- Time to render name section of link id 23919: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.<\/p>\n<!-- Time to render link large description section of link id 23919: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MCL> How to use <\/a>\n<!-- Time to render notes section of link id 23919: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23919: 0.00033879280090332 --> \n<tr><td><a href=\"https:\/\/github.com\/kr-colab\/ReLERNN\" id=\"link-24489\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ReLERNN<\/a>\n<!-- Time to render name section of link id 24489: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Recombination Landscape Estimation using Recurrent Neural Networks<\/p>\n<!-- Time to render link large description section of link id 24489: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ReLERNN> How to use <\/a>\n<!-- Time to render notes section of link id 24489: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24489: 0.0003349781036377 --> \n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/snape-pooled\/\" id=\"link-24089\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snape-pooled<\/a>\n<!-- Time to render name section of link id 24089: 6.9141387939453E-6 --> \n<\/td>\n<td><p>SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.<\/p>\n<!-- Time to render link large description section of link id 24089: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24089: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24089: 0.00033402442932129 --> \n<tr><td><a href=\"http:\/\/membres-timc.imag.fr\/Olivier.Francois\/snmf\/index.htm\" id=\"link-23998\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sNMF<\/a>\n<!-- Time to render name section of link id 23998: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics.<\/p>\n<!-- Time to render link large description section of link id 23998: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23998: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23998: 0.00034618377685547 --> \n<tr><td><a href=\"https:\/\/github.com\/toulbar2\/toulbar2\" id=\"link-24567\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">toulbar2<\/a>\n<!-- Time to render name section of link id 24567: 5.9604644775391E-6 --> \n<\/td>\n<td><p>toulbar2 is an open-source black-box C++ optimizer for cost function networks and discrete additive graphical models. It can read a variety of formats.<\/p>\n<!-- Time to render link large description section of link id 24567: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_toulbar2> How to use <\/a>\n<!-- Time to render notes section of link id 24567: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24567: 0.00033283233642578 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1166\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [field] => term_id\n                            [terms] => 1166\n                            [include_children] => \n                        )\n\n                )\n\n            [post_status] => Array\n                (\n                    [0] => publish\n                )\n\n            [orderby] => Array\n                (\n                    [title] => ASC\n                )\n\n        )\n\n    [query_vars] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] => Array\n                (\n                    [0] => Array\n 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    [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => gapseq\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2026-03-17 10:01:53\n            [post_modified_gmt] => 2026-03-17 09:01:53\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26234\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 1\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    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Time: 0.0012259483337402-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1166 level0\"><!-- Div Category --><div id=\"metabolic-network-modeling\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Metabolic Network Modeling<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/jotech\/gapseq\" id=\"link-26234\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gapseq<\/a>\n<!-- Time to render name section of link id 26234: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks.<\/p>\n<!-- Time to render link large description section of link id 26234: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gapseq> How to use <\/a>\n<!-- Time to render notes section of link id 26234: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26234: 0.00023698806762695 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1162\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => 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[request] => \n\t\t\tSELECT   wp_posts.*\n\t\t\tFROM wp_posts  LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1162)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 24911\n                    [post_author] => 5\n                    [post_date] => 2023-06-22 13:08:14\n                    [post_date_gmt] => 2023-06-22 11:08:14\n                    [post_content] => \n                    [post_title] => HUMAnN\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => humann\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-07-29 08:24:59\n                    [post_modified_gmt] => 2025-07-29 06:24:59\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24911\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 26226\n                    [post_author] => 1\n                    [post_date] => 2026-03-06 17:38:32\n                    [post_date_gmt] => 2026-03-06 16:38:32\n                    [post_content] => \n                    [post_title] => METABOLIC\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => metabolic\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-03-06 17:38:32\n                    [post_modified_gmt] => 2026-03-06 16:38:32\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26226\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 25929\n                    [post_author] => 5\n                    [post_date] => 2025-06-11 09:52:40\n                    [post_date_gmt] => 2025-06-11 07:52:40\n                    [post_content] => \n                    [post_title] => PlantiSMASH\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => plantismash\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-06-25 11:46:06\n                    [post_modified_gmt] => 2025-06-25 09:46:06\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25929\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n        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https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26148\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n        )\n\n    [post_count] => 4\n    [current_post] => -1\n    [in_the_loop] => \n    [post] => WP_Post Object\n        (\n            [ID] => 24911\n            [post_author] => 5\n            [post_date] => 2023-06-22 13:08:14\n            [post_date_gmt] => 2023-06-22 11:08:14\n            [post_content] => \n            [post_title] => HUMAnN\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => humann\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2025-07-29 08:24:59\n            [post_modified_gmt] => 2025-07-29 06:24:59\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24911\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 4\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    [is_category] => \n    [is_tag] => \n    [is_tax] => 1\n    [is_search] => \n    [is_feed] => \n    [is_comment_feed] => \n    [is_trackback] => \n    [is_home] => \n    [is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => cd79a457084e659e0bedfaa284b9094e\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.001168966293335-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1162 level0\"><!-- Div Category --><div id=\"metabolomics\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Metabolomics<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/huttenhower.sph.harvard.edu\/humann\/\" id=\"link-24911\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HUMAnN<\/a>\n<!-- Time to render name section of link id 24911: 8.1062316894531E-6 --> \n<\/td>\n<td><p>HUMAnN is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24911: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HUMAnN> How to use <\/a>\n<!-- Time to render notes section of link id 24911: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24911: 0.00041294097900391 --> \n<tr><td><a href=\"https:\/\/github.com\/AnantharamanLab\/METABOLIC\/wiki\/METABOLIC-Usage\" id=\"link-26226\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">METABOLIC<\/a>\n<!-- Time to render name section of link id 26226: 8.1062316894531E-6 --> \n<\/td>\n<td><p>METabolic And BiogeOchemistry anaLyses In miCrobes<\/p>\n<!-- Time to render link large description section of link id 26226: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_METABOLIC> How to use <\/a>\n<!-- Time to render notes section of link id 26226: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26226: 0.00036287307739258 --> \n<tr><td><a href=\"https:\/\/github.com\/plantismash\/plantismash\" id=\"link-25929\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PlantiSMASH<\/a>\n<!-- Time to render name section of link id 25929: 5.9604644775391E-6 --> \n<\/td>\n<td><p>PlantiSMASH is a specialized extension of antiSMASH for the identification and analysis of biosynthetic gene clusters (BGCs) in plant genomes. It supports advanced plant-specific detection rules and features for comparative genomics, visualization, and more.<\/p>\n<!-- Time to render link large description section of link id 25929: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PlantiSMASH> How to use <\/a>\n<!-- Time to render notes section of link id 25929: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25929: 0.00033712387084961 --> \n<tr><td><a href=\"https:\/\/www.rdkit.org\" id=\"link-26148\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDKit<\/a>\n<!-- Time to render name section of link id 26148: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.<\/p>\n<!-- Time to render link large description section of link id 26148: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RDKit> How to use <\/a>\n<!-- Time to render notes section of link id 26148: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26148: 0.00033402442932129 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1125\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n      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[post_date] => 2022-11-22 10:25:52\n                    [post_date_gmt] => 2022-11-22 09:25:52\n                    [post_content] => \n                    [post_title] => circtools\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => circtools\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:10:05\n                    [post_modified_gmt] => 2025-05-21 06:10:05\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/circtools\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                  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href=\"http:\/\/mbio-serv2.mbioekol.lu.se\/ARAGORN\/\" id=\"link-23587\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARAGORN<\/a>\n<!-- Time to render name section of link id 23587: 5.9604644775391E-6 --> \n<\/td>\n<td><p>ARAGORN is a program to detect tRNA genes and tmRNA genes in nucleotide sequence<\/p>\n<!-- Time to render link large description section of link id 23587: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23587: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23587: 0.00028491020202637 --> \n<tr><td><a href=\"http:\/\/www.vicbioinformatics.com\/software.shtml\" id=\"link-23591\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Barrnap<\/a>\n<!-- Time to render name section of link id 23591: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).<\/p>\n<!-- Time to render link large description section of link id 23591: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23591: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23591: 0.00031900405883789 --> \n<tr><td><a href=\"https:\/\/github.com\/pavanvidem\/blockclust\" id=\"link-24025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BlockClust<\/a>\n<!-- Time to render name section of link id 24025: 5.0067901611328E-6 --> \n<\/td>\n<td><p>BlockClust is an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. BlockClust allows both clustering and classification of small non-coding RNAs.<\/p>\n<!-- Time to render link large description section of link id 24025: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24025: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24025: 0.00025820732116699 --> \n<tr><td><a href=\"https:\/\/github.com\/dieterich-lab\/circtools\" id=\"link-24117\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">circtools<\/a>\n<!-- Time to render name section of link id 24117: 5.9604644775391E-6 --> \n<\/td>\n<td><p>A modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.<\/p>\n<!-- Time to render link large description section of link id 24117: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24117: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24117: 0.0002589225769043 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfo-biols\/CIRI-long\" id=\"link-24179\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CIRI-long<\/a>\n<!-- Time to render name section of link id 24179: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Circular RNA Identification for Long-Reads Nanopore Sequencing Data.<\/p>\n<!-- Time to render link large description section of link id 24179: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CIRI-long> How to use <\/a>\n<!-- Time to render notes section of link id 24179: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24179: 0.00027203559875488 --> \n<tr><td><a href=\"https:\/\/github.com\/MikeAxtell\/CleaveLand4\" id=\"link-24110\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CleaveLand4<\/a>\n<!-- Time to render name section of link id 24110: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Analysis of degradome data to find sliced miRNA and siRNA targets<\/p>\n<!-- Time to render link large description section of link id 24110: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CleaveLand4> How to use <\/a>\n<!-- Time to render notes section of link id 24110: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24110: 0.00026702880859375 --> \n<tr><td><a href=\"https:\/\/github.com\/tderrien\/FEELnc\" id=\"link-23778\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FEELnc<\/a>\n<!-- Time to render name section of link id 23778: 5.0067901611328E-6 --> \n<\/td>\n<td><p>FlExible Extraction of LncRNA.<\/p>\n<!-- Time to render link large description section of link id 23778: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FEELnc> How to use <\/a\n<!-- Time to render notes section of link id 23778: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23778: 0.00025200843811035 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/infernal\/\" id=\"link-23648\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Infernal<\/a>\n<!-- Time to render name section of link id 23648: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).<\/p>\n<!-- Time to render link large description section of link id 23648: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Infernal> How to use <\/a>\n<!-- Time to render notes section of link id 23648: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23648: 0.00025701522827148 --> \n<tr><td><a href=\"https:\/\/www.mdc-berlin.de\/n-rajewsky#t-data,software&#038;resources\" id=\"link-23668\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">miRDeep2<\/a>\n<!-- Time to render name section of link id 23668: 5.0067901611328E-6 --> \n<\/td>\n<td><p>miRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples. Last, a new module for preprocessing of raw Illumina sequencing data produces files for downstream analysis with the miRDeep2 or quantifier module.<\/p>\n<!-- Time to render link large description section of link id 23668: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_miRDeep2> How to use <\/a>\n<!-- Time to render notes section of link id 23668: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23668: 0.00026702880859375 --> \n<tr><td><a href=\"http:\/\/wwwabi.snv.jussieu.fr\/research\/publi\/small_ncRNA\/\" id=\"link-23875\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiRfold<\/a>\n<!-- Time to render name section of link id 23875: 5.0067901611328E-6 --> \n<\/td>\n<td><p>MiRfold searches for a good miRNA-like folding in the sequence surrounding a putative miRNA. It was optimized on plant miRNAs.<\/p>\n<!-- Time to render link large description section of link id 23875: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23875: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23875: 0.00027084350585938 --> \n<tr><td><a href=\"http:\/\/www.bioinf.man.ac.uk\/resources\/phase\/\" id=\"link-23772\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHASE<\/a>\n<!-- Time to render name section of link id 23772: 3.814697265625E-6 --> \n<\/td>\n<td><p>PHASE is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.<\/p>\n<!-- Time to render link large description section of link id 23772: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHASE> How to use <\/a>\n<!-- Time to render notes section of link id 23772: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23772: 0.00025391578674316 --> \n<tr><td><a href=\"http:\/\/phasetank.sourceforge.net\" id=\"link-24440\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhaseTank<\/a>\n<!-- Time to render name section of link id 24440: 5.0067901611328E-6 --> \n<\/td>\n<td><p>To systemically characterize phasiRNAs\/tasiRNAs and their regulatory cascades 'miRNA\/phasiRNA -&amp;gt<\/p>\n<!-- Time to render link large description section of link id 24440: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24440: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24440: 0.00025200843811035 --> \n<tr><td><a href=\"http:\/\/hrgv.github.io\/phyloFlash\" id=\"link-25094\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phyloFlash<\/a>\n<!-- Time to render name section of link id 25094: 5.0067901611328E-6 --> \n<\/td>\n<td><p>phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.<\/p>\n<!-- Time to render link large description section of link id 25094: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_phyloFlash> How to use <\/a>\n<!-- Time to render notes section of link id 25094: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25094: 0.00025510787963867 --> \n<tr><td><a href=\"https:\/\/github.com\/suhrig\/pingpongpro\" id=\"link-24449\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PingPongPro<\/a>\n<!-- Time to render name section of link id 24449: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Find ping-pong signatures in piRNA-Seq data like a pro.<\/p>\n<!-- Time to render link large description section of link id 24449: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24449: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24449: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/prost.readthedocs.io\" id=\"link-25118\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Prost<\/a>\n<!-- Time to render name section of link id 25118: 2.1457672119141E-6 --> \n<\/td>\n<td><p><em>Prost!<\/em>\u00a0(PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform.\u00a0<em>Prost!<\/em>\u00a0does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single\u00a0<em>Prost!<\/em>\u00a0run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location,\u00a0<em>Prost!<\/em>\u00a0then annotates them using a user-defined annotation database (public or personal annotation database).<\/p>\n<!-- Time to render link large description section of link id 25118: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Prost> How to use <\/a>\n<!-- Time to render notes section of link id 25118: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25118: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-leipzig.de\/~kristin\/Software\/RNAclust\/\" id=\"link-24499\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAclust<\/a>\n<!-- Time to render name section of link id 24499: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif.<\/p>\n<!-- Time to render link large description section of link id 24499: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24499: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24499: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/services.healthtech.dtu.dk\/services\/RNAmmer-1.2\/\" id=\"link-23719\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAmmer<\/a>\n<!-- Time to render name section of link id 23719: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Rnammer predicts 5s\/8s, 16s\/18s, and 23s\/28s ribosomal RNA in tttfull genome sequences. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project.<\/p>\n<!-- Time to render link large description section of link id 23719: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RNAmmer> How to use <\/a>\n<!-- Time to render notes section of link id 23719: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23719: 0.00011491775512695 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-freiburg.de\/Software\/RNAscClust\/\" id=\"link-24500\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAscClust<\/a>\n<!-- Time to render name section of link id 24500: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RNAscClust is a pipeline to cluster a set of structured RNAs taking their respective structural conservation into account. The aim of RNAscClust is to aid the discovery of families and classes of ncRNAs.<\/p>\n<!-- Time to render link large description section of link id 24500: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24500: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24500: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/MikeAxtell\/ShortStack\" id=\"link-23727\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ShortStack<\/a>\n<!-- Time to render name section of link id 23727: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.<\/p>\n<!-- Time to render link large description section of link id 23727: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ShortStack> How to use <\/a>\n<!-- Time to render notes section of link id 23727: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23727: 0.0001068115234375 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/snoGPS\/\" id=\"link-25293\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snoGPS<\/a>\n<!-- Time to render name section of link id 25293: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Search for H\/ACA snoRNA genes in a genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 25293: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_snoGPS> How to use <\/a>\n<!-- Time to render notes section of link id 25293: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25293: 0.00011587142944336 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/snoscan\" id=\"link-25262\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Snoscan<\/a>\n<!-- Time to render name section of link id 25262: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Search for C\/D box methylation guide snoRNA genes in a genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 25262: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Snoscan> How to use <\/a>\n<!-- Time to render notes section of link id 25262: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25262: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/bioinfo.lifl.fr\/RNA\/sortmerna\/index.php\" id=\"link-23734\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SortMeRNA<\/a>\n<!-- Time to render name section of link id 23734: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity<\/p>\n<!-- Time to render link large description section of link id 23734: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SortMeRNA> How to use <\/a>\n<!-- Time to render notes section of link id 23734: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23734: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/mzytnicki\/srnaMapper\" id=\"link-24541\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">srnaMapper<\/a>\n<!-- Time to render name section of link id 24541: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This tool maps reads produced by sRNA-Seq to a genome.<\/p>\n<!-- Time to render link large description section of link id 24541: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24541: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24541: 0.00011610984802246 --> \n<tr><td><a href=\"http:\/\/lowelab.ucsc.edu\/tRNAscan-SE\/\" id=\"link-23757\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">tRNAscan-SE<\/a>\n<!-- Time to render name section of link id 23757: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Search for tRNA genes in genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 23757: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_tRNAscan-SE> How to use <\/a>\n<!-- Time to render notes section of link id 23757: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23757: 0.00010800361633301 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] 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       (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0018439292907715-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1133 level0\"><!-- Div Category --><div id=\"nucleic-acid-folding\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Nucleic acid folding<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"http:\/\/aidenlab.org\/juicebox\/\" id=\"link-23797\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Juicebox<\/a>\n<!-- Time to render name section of link id 23797: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Software for visualizing data from Hi-C and other proximity mapping experiments<\/p>\n<!-- Time to render link large description section of link id 23797: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23797: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23797: 0.00035405158996582 --> \n<tr><td><a href=\"https:\/\/github.com\/theaidenlab\/juicer\/\" id=\"link-23784\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Juicer<\/a>\n<!-- Time to render name section of link id 23784: 5.9604644775391E-6 --> \n<\/td>\n<td><p>A One-Click System for Analyzing Loop-Resolution Hi-C Experiments<\/p>\n<!-- Time to render link large description section of link id 23784: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Juicer> How to use <\/a>\n<!-- Time to render notes section of link id 23784: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23784: 0.00033688545227051 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-freiburg.de\/Software\/LocARNA\/\" id=\"link-24351\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LocARNA<\/a>\n<!-- Time to render name section of link id 24351: 6.9141387939453E-6 --> \n<\/td>\n<td><p>LocARNA is a tool for multiple alignment of RNA molecules. LocARNA requires only RNA sequences as input and will simultaneously fold and align the input sequences.<\/p>\n<!-- Time to render link large description section of link id 24351: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24351: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24351: 0.00033402442932129 --> \n<tr><td><a href=\"http:\/\/wwwabi.snv.jussieu.fr\/research\/publi\/small_ncRNA\/\" id=\"link-23875\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiRfold<\/a>\n<!-- Time to render name section of link id 23875: 5.9604644775391E-6 --> \n<\/td>\n<td><p>MiRfold searches for a good miRNA-like folding in the sequence surrounding a putative miRNA. It was optimized on plant miRNAs.<\/p>\n<!-- Time to render link large description section of link id 23875: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23875: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23875: 0.00035309791564941 --> \n<tr><td><a href=\"https:\/\/github.com\/abcsFrederick\/non-B_gfa\" id=\"link-24418\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">non-B_gfa<\/a>\n<!-- Time to render name section of link id 24418: 7.1525573730469E-6 --> \n<\/td>\n<td><p>gfa programs for Non-B site at NCI\/FNLCR. gfa is a Suite of programs developed at NCI-Frederick\/Frederick National Lab to find sequences associated with non-B DNA forming motifs.<\/p>\n<!-- Time to render link large description section of link id 24418: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24418: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24418: 0.00033903121948242 --> \n<tr><td><a href=\"https:\/\/github.com\/aqlaboratory\/openfold-3\" id=\"link-26159\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Openfold3<\/a>\n<!-- Time to render name section of link id 26159: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A fully open source biomolecular structure prediction model based on AlphaFold3.<\/p>\n<!-- Time to render link large description section of link id 26159: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Openfold3> How to use <\/a>\n<!-- Time to render notes section of link id 26159: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26159: 0.0003359317779541 --> \n<tr><td><a href=\"https:\/\/rth.dk\/resources\/petfold\/\" id=\"link-24436\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PETfold<\/a>\n<!-- Time to render name section of link id 24436: 6.9141387939453E-6 --> \n<\/td>\n<td><p>PETfold performs Probabilistic Evolutionary and Thermodynamic folding of a multiple alignment of RNA sequences.<\/p>\n<!-- Time to render link large description section of link id 24436: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24436: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24436: 0.00033187866210938 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/R-scape\/\" id=\"link-24476\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">R-scape<\/a>\n<!-- Time to render name section of link id 24476: 5.9604644775391E-6 --> \n<\/td>\n<td><p>R-scape looks for evidence of a conserved RNA structure by measuring pairwise covariations observed in an input multiple sequence alignment. It analyzes all possible pairs, including those in your proposed structure (if you provide one).<\/p>\n<!-- Time to render link large description section of link id 24476: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24476: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24476: 0.00035905838012695 --> \n<tr><td><a href=\"http:\/\/bioinformatics.psb.ugent.be\/supplementary_data\/erbon\/nov2003\/\" id=\"link-23907\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">randfold<\/a>\n<!-- Time to render name section of link id 23907: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The software compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences..<\/p>\n<!-- Time to render link large description section of link id 23907: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_randfold> How to use <\/a>\n<!-- Time to render notes section of link id 23907: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23907: 0.00034904479980469 --> \n<tr><td><a href=\"https:\/\/github.com\/RosettaCommons\/RFdiffusion\" id=\"link-26170\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RFdiffusion<\/a>\n<!-- Time to render name section of link id 26170: 6.9141387939453E-6 --> \n<\/td>\n<td><p>RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc).<\/p>\n<!-- Time to render link large description section of link id 26170: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RFdiffusion> How to use <\/a>\n<!-- Time to render notes section of link id 26170: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26170: 0.0005040168762207 --> \n<tr><td><a href=\"https:\/\/www.ncrna.org\/softwares\/rfold\/\" id=\"link-24495\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Rfold<\/a>\n<!-- Time to render name section of link id 24495: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Rfold computes local base pairing probabilities for long DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 24495: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24495: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24495: 0.00034093856811523 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-leipzig.de\/~kristin\/Software\/RNAclust\/\" id=\"link-24499\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAclust<\/a>\n<!-- Time to render name section of link id 24499: 6.9141387939453E-6 --> \n<\/td>\n<td><p>RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif.<\/p>\n<!-- Time to render link large description section of link id 24499: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24499: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24499: 0.00035309791564941 --> \n<tr><td><a href=\"https:\/\/www.tbi.univie.ac.at\/software\/RNAz\/\" id=\"link-24501\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAz<\/a>\n<!-- Time to render name section of link id 24501: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RNAz detects stable and conserved RNA secondary structures in multiple sequence alignments.<\/p>\n<!-- Time to render link large description section of link id 24501: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24501: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24501: 0.00013494491577148 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1138\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => 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10:26:10\n            [post_date_gmt] => 2022-11-22 09:26:10\n            [post_content] => \n            [post_title] => ASHURE\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => ashure\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2025-05-21 07:28:43\n            [post_modified_gmt] => 2025-05-21 05:28:43\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/ashure\/\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 32\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    [is_category] => \n    [is_tag] => \n    [is_tax] => 1\n    [is_search] => \n    [is_feed] => \n    [is_comment_feed] => \n    [is_trackback] => \n    [is_home] => \n    [is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => a7a0b1fcd2817f4cab161bc335182574\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0023348331451416-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1138 level0\"><!-- Div Category --><div id=\"ont\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">ONT<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/BBaloglu\/ASHURE\" id=\"link-24145\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASHURE<\/a>\n<!-- Time to render name section of link id 24145: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Python-based pipeline for analyzing Nanopore sequencing metabarcoding data. ASHURE can take a reference database in order to improve accuracy.<\/p>\n<!-- Time to render link large description section of link id 24145: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24145: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24145: 0.00029897689819336 --> \n<tr><td><a href=\"https:\/\/github.com\/Psy-Fer\/blue-crab\" id=\"link-25792\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">blue-crab<\/a>\n<!-- Time to render name section of link id 25792: 4.7683715820312E-6 --> \n<\/td>\n<td><p>blue-crab is a conversion tool to convert from ONT's POD5 format to the community maintained SLOW5\/BLOW5 format.<\/p>\n<!-- Time to render link large description section of link id 25792: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_blue-crab> How to use <\/a>\n<!-- Time to render notes section of link id 25792: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25792: 0.00028395652770996 --> \n<tr><td><a href=\"https:\/\/github.com\/kamimrcht\/CARNAC-LR\" id=\"link-24000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CARNAC-LR<\/a>\n<!-- Time to render name section of link id 24000: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Clustering coefficient-based Acquisition of RNA Communities in Long Reads.<\/p>\n<!-- Time to render link large description section of link id 24000: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24000: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24000: 0.00027799606323242 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/chopper\" id=\"link-25324\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chopper<\/a>\n<!-- Time to render name section of link id 25324: 5.0067901611328E-6 --> \n<\/td>\n<td><p>This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.<\/p>\r\n<p>chopper is a tool that reunites the now outdated softwares NanoFilt and NanoLyse. It permits to filter QC files and has a faster execution time than NanoFilt and NanoLyse.<\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 25324: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chopper> How to use <\/a>\n<!-- Time to render notes section of link id 25324: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25324: 0.00028204917907715 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/CONSENT\" id=\"link-24079\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CONSENT<\/a>\n<!-- Time to render name section of link id 24079: 2.0027160644531E-5 --> \n<\/td>\n<td><p>CONSENT (sCalable self-cOrrectioN of long reads with multiple SEquence alignmeNT) is a self-correction method for long reads.<\/p>\n<!-- Time to render link large description section of link id 24079: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24079: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24079: 0.00029206275939941 --> \n<tr><td><a href=\"https:\/\/github.com\/MartinPippel\/DAmar\" id=\"link-24191\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAmar<\/a>\n<!-- Time to render name section of link id 24191: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Long read QC, assembly and scaffolding pipeline for PacBio or Oxford Nanopore long-read sequencing data. T he pipeline produces a number of QC metrics at various stages as well as incorporating further technologies including Bionano, 10x and HiC data to scaffold the created contigs. DAmar, is a hybrid of the earlier Marvel, Dazzler, and Daccord systems of the Eugene Myers lab.<\/p>\n<!-- Time to render link large description section of link id 24191: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24191: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24191: 0.00028800964355469 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Deepbinner\" id=\"link-24010\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Deepbinner<\/a>\n<!-- Time to render name section of link id 24010: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porechop), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads.<\/p>\n<!-- Time to render link large description section of link id 24010: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24010: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24010: 0.00027918815612793 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfomaticsCSU\/deepsignal\" id=\"link-24197\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepSignal<\/a>\n<!-- Time to render name section of link id 24197: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Detecting methylation using signal-level features from Nanopore sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24197: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24197: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24197: 0.00027704238891602 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/dorado\" id=\"link-24899\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Dorado<\/a>\n<!-- Time to render name section of link id 24899: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.<\/p>\n<!-- Time to render link large description section of link id 24899: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Dorado> How to use <\/a>\n<!-- Time to render notes section of link id 24899: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24899: 0.00022721290588379 --> \n<tr><td><a href=\"https:\/\/github.com\/hasindu2008\/f5c\" id=\"link-25793\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">f5c<\/a>\n<!-- Time to render name section of link id 25793: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Ultra-fast methylation calling and event alignment tool for nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25793: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_f5c> How to use <\/a>\n<!-- Time to render notes section of link id 25793: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25793: 0.00015401840209961 --> \n<tr><td><a href=\"https:\/\/github.com\/fenderglass\/Flye\" id=\"link-24015\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Flye<\/a>\n<!-- Time to render name section of link id 24015: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.<\/p>\n<!-- Time to render link large description section of link id 24015: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Flye> How to use <\/a>\n<!-- Time to render notes section of link id 24015: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24015: 0.0001518726348877 --> \n<tr><td><a href=\"https:\/\/github.com\/yeeus\/GCI.git\" id=\"link-25561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GCI<\/a>\n<!-- Time to render name section of link id 25561: 3.0994415283203E-6 --> \n<\/td>\n<td>Genome Continuity Inspector (GCI) is an assembly assessment tool for high-quality genomes (e.g. T2T genomes), in base resolution.\n<!-- Time to render link large description section of link id 25561: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCI> How to use <\/a>\n<!-- Time to render notes section of link id 25561: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25561: 0.00020599365234375 --> \n<tr><td><a href=\"http:\/\/www.fishbrowser.org\/software\/LR_Gapcloser\/index.php\/Home\/Index\/Index.html\" id=\"link-24030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LR_Gapcloser<\/a>\n<!-- Time to render name section of link id 24030: 3.0994415283203E-6 --> \n<\/td>\n<td><p>\u00a0LR_Gapcloser is a gap closing tool using uncorrected or corrected long reads generated from Pacbio platform or Nanopore platform.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24030: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24030: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24030: 0.00014591217041016 --> \n<tr><td><a href=\"https:\/\/github.com\/al-mcintyre\/mCaller\" id=\"link-24063\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mCaller<\/a>\n<!-- Time to render name section of link id 24063: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This program is designed to call m6A from nanopore data using the differences between measured and expected currents.<\/p>\n<!-- Time to render link large description section of link id 24063: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24063: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24063: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/epi2me-labs\/modbam2bed\" id=\"link-24714\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">modbam2bed<\/a>\n<!-- Time to render name section of link id 24714: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.<\/p>\n<!-- Time to render link large description section of link id 24714: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_modbam2bed> How to use <\/a>\n<!-- Time to render notes section of link id 24714: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24714: 0.00014495849609375 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/modkit\" id=\"link-25325\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Modkit<\/a>\n<!-- Time to render name section of link id 25325: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics.<\/p>\n<!-- Time to render link large description section of link id 25325: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Modkit> How to use <\/a>\n<!-- Time to render notes section of link id 25325: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25325: 0.00015497207641602 --> \n<tr><td><a href=\"https:\/\/github.com\/PrestonLeung\/Nano-Q\" id=\"link-24405\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Nano-Q<\/a>\n<!-- Time to render name section of link id 24405: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Python script for conservatively cleaning ONT reads from bam files and estimate variant frequencies.<\/p>\n<!-- Time to render link large description section of link id 24405: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24405: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24405: 0.00014400482177734 --> \n<tr><td><a href=\"https:\/\/github.com\/ImagoXV\/NanoASV\/tree\/main\" id=\"link-25782\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoASV<\/a>\n<!-- Time to render name section of link id 25782: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Nanopore full-length 16S metabarcoding amplicon data analysis<\/p>\n<!-- Time to render link large description section of link id 25782: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoASV> How to use <\/a>\n<!-- Time to render notes section of link id 25782: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25782: 0.00014805793762207 --> \n<tr><td><a href=\"https:\/\/github.com\/genomicsITER\/NanoCLUST\" id=\"link-24407\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCLUST<\/a>\n<!-- Time to render name section of link id 24407: 2.8610229492188E-6 --> \n<\/td>\n<td><p>NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads.<\/p>\n<!-- Time to render link large description section of link id 24407: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoCLUST> How to use <\/a>\n<!-- Time to render notes section of link id 24407: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24407: 0.00014686584472656 --> \n<tr><td><a href=\"https:\/\/github.com\/a-slide\/NanoCount\" id=\"link-24408\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCount<\/a>\n<!-- Time to render name section of link id 24408: 2.8610229492188E-6 --> \n<\/td>\n<td><p>NanoCount estimates transcripts abundance from Oxford Nanopore direct-RNA sequencing datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads.<\/p>\n<!-- Time to render link large description section of link id 24408: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24408: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24408: 0.00014495849609375 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/NanoSim\" id=\"link-24029\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoSim<\/a>\n<!-- Time to render name section of link id 24029: 2.8610229492188E-6 --> \n<\/td>\n<td><p>NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology.<\/p>\n<!-- Time to render link large description section of link id 24029: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoSim> How to use <\/a>\n<!-- Time to render notes section of link id 24029: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24029: 0.00014901161193848 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/NECAT\" id=\"link-24411\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NECAT<\/a>\n<!-- Time to render name section of link id 24411: 3.0994415283203E-6 --> \n<\/td>\n<td><p>NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.<\/p>\n<!-- Time to render link large description section of link id 24411: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NECAT> How to use <\/a>\n<!-- Time to render notes section of link id 24411: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24411: 0.00014519691467285 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/ont_fast5_api\" id=\"link-24086\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ont_fast5_api<\/a>\n<!-- Time to render name section of link id 24086: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore fast5 file format.<\/p>\n<!-- Time to render link large description section of link id 24086: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ont_fast5_api> How to use <\/a>\n<!-- Time to render notes section of link id 24086: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24086: 0.00018000602722168 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/pod5-file-format\" id=\"link-25791\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">POD5<\/a>\n<!-- Time to render name section of link id 25791: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The pod5 Python package contains the tools and python API wrapping the compiled bindings for the POD5 file format from lib_pod5.<\/p>\n<!-- Time to render link large description section of link id 25791: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_POD5> How to use <\/a>\n<!-- Time to render notes section of link id 25791: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25791: 0.00014519691467285 --> \n<tr><td><a href=\"https:\/\/github.com\/bonsai-team\/Porechop_ABI\" id=\"link-24099\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Porechop_ABI<\/a>\n<!-- Time to render name section of link id 24099: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Porechop_abi (ab initio) is an extension of Porechop that is able to infer the adapter sequence from the Oxford Nanopore reads. It discovers the adapter sequence from the reads using approximate k-mers and assembly, and add the sequence found to the adapter list (adapters.py file).<\/p>\n<!-- Time to render link large description section of link id 24099: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Porechop_ABI> How to use <\/a>\n<!-- Time to render notes section of link id 24099: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24099: 0.00014209747314453 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/Ratatosk\" id=\"link-24485\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ratatosk<\/a>\n<!-- Time to render name section of link id 24485: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Ratatosk is a phased error correction tool for erroneous long reads based on compacted and colored de Bruijn graphs built from accurate short reads.<\/p>\n<!-- Time to render link large description section of link id 24485: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24485: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24485: 0.00014591217041016 --> \n<tr><td><a href=\"https:\/\/github.com\/paoloshasta\/shasta\" id=\"link-24118\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Shasta<\/a>\n<!-- Time to render name section of link id 24118: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.<\/p>\n<!-- Time to render link large description section of link id 24118: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Shasta> How to use <\/a>\n<!-- Time to render notes section of link id 24118: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24118: 0.00014495849609375 --> \n<tr><td><a href=\"https:\/\/github.com\/fritzsedlazeck\/Sniffles\" id=\"link-24524\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sniffles<\/a>\n<!-- Time to render name section of link id 24524: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.<\/p>\n<!-- Time to render link large description section of link id 24524: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sniffles> How to use <\/a>\n<!-- Time to render notes section of link id 24524: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24524: 0.00014591217041016 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/spliced_bam2gff\" id=\"link-24605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spliced_bam2gff<\/a>\n<!-- Time to render name section of link id 24605: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A tool to convert spliced BAM alignments into GFF2 format.<\/p>\n<!-- Time to render link large description section of link id 24605: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24605: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24605: 0.00014710426330566 --> \n<tr><td><a href=\"https:\/\/github.com\/Psy-Fer\/SquiggleKit\" id=\"link-24127\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SquiggleKit<\/a>\n<!-- Time to render name section of link id 24127: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A toolkit for manipulating nanopore signal data.<\/p>\n<!-- Time to render link large description section of link id 24127: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24127: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24127: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/tombo\" id=\"link-24011\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tombo<\/a>\n<!-- Time to render name section of link id 24011: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24011: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24011: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24011: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/treangenlab\/variabel\" id=\"link-24575\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Variabel<\/a>\n<!-- Time to render name section of link id 24575: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A novel approach and method for intrahost variant detection, which outperforms existing ONT variant callers.<\/p>\n<!-- Time to render link large description section of link id 24575: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24575: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24575: 0.0001068115234375 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    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render name section of link id 25521: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Bandage-NG is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as SPAdes, MEGAHIT and others.<\/p>\n<!-- Time to render link large description section of link id 25521: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bandage-NG> How to use <\/a>\n<!-- Time to render notes section of link id 25521: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25521: 0.00012898445129395 --> \n<tr><td><a href=\"https:\/\/github.com\/pmelsted\/bifrost\" id=\"link-24997\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bifrost<\/a>\n<!-- Time to render name section of link id 24997: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Highly parallel construction and indexing of colored and compacted de Bruijn graphs.<\/p>\n<!-- Time to render link large description section of link id 24997: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bifrost> How to use <\/a>\n<!-- Time to render notes section of link id 24997: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24997: 0.00012922286987305 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/cactus\" id=\"link-24984\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cactus<\/a>\n<!-- Time to render name section of link id 24984: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit.<\/p>\n<!-- Time to render link large description section of link id 24984: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cactus> How to use <\/a>\n<!-- Time to render notes section of link id 24984: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24984: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/fastix\" id=\"link-25004\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastix<\/a>\n<!-- Time to render name section of link id 25004: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A simple command line tool to add prefixes to FASTA headers.<\/p>\n<!-- Time to render link large description section of link id 25004: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastix> How to use <\/a>\n<!-- Time to render notes section of link id 25004: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25004: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/marschall-lab\/gaftools\" id=\"link-26161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gaftools<\/a>\n<!-- Time to render name section of link id 26161: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gaftools is a fast and comprehensive toolkit designed for processing pangenome alignments.<\/p>\n<!-- Time to render link large description section of link id 26161: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gaftools> How to use <\/a>\n<!-- Time to render notes section of link id 26161: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26161: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/github.com\/snurk\/gfacpp\" id=\"link-26114\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gfacpp<\/a>\n<!-- Time to render name section of link id 26114: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Library for common operations on GFA graphs and some processing algorithms.<\/p>\n<!-- Time to render link large description section of link id 26114: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gfacpp> How to use <\/a>\n<!-- Time to render notes section of link id 26114: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26114: 0.00015783309936523 --> \n<tr><td><a href=\"https:\/\/github.com\/marschall-lab\/GFAffix\" id=\"link-25428\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GFAffix<\/a>\n<!-- Time to render name section of link id 25428: 2.1457672119141E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25428: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GFAffix> How to use <\/a>\n<!-- Time to render notes section of link id 25428: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25428: 0.00010490417480469 --> \n<tr><td><a href=\"https:\/\/github.com\/ggonnella\/gfaviz\" id=\"link-25600\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GfaViz<\/a>\n<!-- Time to render name section of link id 25600: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Graphical interactive tool for the visualization of sequence graphs in GFA format.<\/p>\n<!-- Time to render link large description section of link id 25600: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GfaViz> How to use <\/a>\n<!-- Time to render notes section of link id 25600: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25600: 0.00010490417480469 --> \n<tr><td><a href=\"https:\/\/github.com\/bacpop\/ggCaller\" id=\"link-25574\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ggCaller<\/a>\n<!-- Time to render name section of link id 25574: 1.9073486328125E-6 --> \n<\/td>\n<td>A de Bruijn graph-based gene-caller and pangenome analysis tool.\n<!-- Time to render link large description section of link id 25574: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ggCaller> How to use <\/a>\n<!-- Time to render notes section of link id 25574: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25574: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/forge.ird.fr\/diade\/dynadiv\/grannot\" id=\"link-25728\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GrAnnoT<\/a>\n<!-- Time to render name section of link id 25728: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GrAnnoT is an annotation transfer tool for pangenome graphs.<\/p>\n<!-- Time to render link large description section of link id 25728: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GrAnnoT> How to use <\/a>\n<!-- Time to render notes section of link id 25728: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25728: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/hal2vg\" id=\"link-25449\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hal2vg<\/a>\n<!-- Time to render name section of link id 25449: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Convert HAL to vg-compatible sequence graph.<\/p>\n<!-- Time to render link large description section of link id 25449: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hal2vg> How to use <\/a>\n<!-- Time to render notes section of link id 25449: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25449: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/mkirsche\/Jasmine\" id=\"link-25042\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jasmine<\/a>\n<!-- Time to render name section of link id 25042: 1.9073486328125E-6 --> \n<\/td>\n<td><p dir=\"auto\">JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges. This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.<\/p>\r\n<p dir=\"auto\">Manual : <a href=\"https:\/\/github.com\/mkirsche\/Jasmine\/wiki\/Jasmine-User-Manual\">Jasmine User Manual \u00b7 mkirsche\/Jasmine Wiki \u00b7 GitHub<\/a><\/p>\r\n<p dir=\"auto\">Jasmine also includes a module for automating the creation of\u00a0<a href=\"http:\/\/software.broadinstitute.org\/software\/igv\/\" rel=\"nofollow\">IGV<\/a>\u00a0screenshots of variants of interest.<\/p>\n<!-- Time to render link large description section of link id 25042: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Jasmine> How to use <\/a>\n<!-- Time to render notes section of link id 25042: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25042: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/ksnp\/\" id=\"link-25283\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kSNP4<\/a>\n<!-- Time to render name section of link id 25283: 2.1457672119141E-6 --> \n<\/td>\n<td><p>kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.<\/p>\n<!-- Time to render link large description section of link id 25283: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kSNP4> How to use <\/a>\n<!-- Time to render notes section of link id 25283: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25283: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/pangenome\/odgi\" id=\"link-24424\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">odgi<\/a>\n<!-- Time to render name section of link id 24424: 1.9073486328125E-6 --> \n<\/td>\n<td><p>odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses.<\/p>\n<!-- Time to render link large description section of link id 24424: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_odgi> How to use <\/a>\n<!-- Time to render notes section of link id 24424: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24424: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/gem-pasteur\/PanACoTA\" id=\"link-26201\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanACoTA<\/a>\n<!-- Time to render name section of link id 26201: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PANgenome with Annotations, COre identification, Tree and corresponding Alignments.<\/p>\n<!-- Time to render link large description section of link id 26201: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanACoTA> How to use <\/a>\n<!-- Time to render notes section of link id 26201: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26201: 0.00013518333435059 --> \n<tr><td><a href=\"https:\/\/github.com\/marschall-lab\/panacus\" id=\"link-25448\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">panacus<\/a>\n<!-- Time to render name section of link id 25448: 2.1457672119141E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25448: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_panacus> How to use <\/a>\n<!-- Time to render notes section of link id 25448: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25448: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/eblerjana\/pangenie\" id=\"link-24960\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanGenie<\/a>\n<!-- Time to render name section of link id 24960: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph.<\/p>\n<!-- Time to render link large description section of link id 24960: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanGenie> How to use <\/a>\n<!-- Time to render notes section of link id 24960: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24960: 0.00010085105895996 --> \n<tr><td><a href=\"https:\/\/github.com\/piosierra\/pantera\" id=\"link-26096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pantera<\/a>\n<!-- Time to render name section of link id 26096: 2.1457672119141E-6 --> \n<\/td>\n<td><p class=\"heading-element\" dir=\"auto\">Identification of transposable element families from pangenome polymorphisms. A pangenome is a collection of genomes or haplotypes that can be aligned and stored as a variation graph in gfa format. pantera receives as input a list of gfa files of non overlapping variation graphs and produces a library of transposable elements found to be polymorphic on that pangenome.<\/p>\n<!-- Time to render link large description section of link id 26096: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pantera> How to use <\/a>\n<!-- Time to render notes section of link id 26096: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26096: 9.8228454589844E-5 --> \n<tr><td><a href=\"https:\/\/pantools.readthedocs.io\/en\/latest\/\" id=\"link-25000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanTools<\/a>\n<!-- Time to render name section of link id 25000: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PanTools is a toolkit for comparative analysis of large number of genomes.<\/p>\n<!-- Time to render link large description section of link id 25000: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanTools> How to use <\/a>\n<!-- Time to render notes section of link id 25000: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25000: 9.7036361694336E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/pangenome\/pggb\" id=\"link-24887\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pggb<\/a>\n<!-- Time to render name section of link id 24887: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pangenome graph builder.<\/p>\n<!-- Time to render link large description section of link id 24887: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pggb> How to use <\/a>\n<!-- Time to render notes section of link id 24887: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24887: 0.00012493133544922 --> \n<tr><td><a href=\"https:\/\/github.com\/kehrlab\/PopIns2\" id=\"link-24998\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PopIns2<\/a>\n<!-- Time to render name section of link id 24998: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs.<\/p>\n<!-- Time to render link large description section of link id 24998: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24998: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24998: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/labgem\/PPanGGOLiN\" id=\"link-25706\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PPanGGOLiN<\/a>\n<!-- Time to render name section of link id 25706: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations.<\/p>\n<!-- Time to render link large description section of link id 25706: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PPanGGOLiN> How to use <\/a>\n<!-- Time to render notes section of link id 25706: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25706: 0.00012302398681641 --> \n<tr><td><a href=\"https:\/\/github.com\/isabelschober\/proteinortho_curves\" id=\"link-25230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">proteinortho_curves<\/a>\n<!-- Time to render name section of link id 25230: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Draw pan- and core-genome curves from proteinortho output<\/p>\n<!-- Time to render link large description section of link id 25230: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_proteinortho_curves> How to use <\/a>\n<!-- Time to render notes section of link id 25230: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25230: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/JiaoLab2021\/varigraph\" id=\"link-26195\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">varigraph<\/a>\n<!-- Time to render name section of link id 26195: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes.<\/p>\n<!-- Time to render link large description section of link id 26195: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_varigraph> How to use <\/a>\n<!-- Time to render notes section of link id 26195: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26195: 0.00014400482177734 --> \n<tr><td><a href=\"https:\/\/github.com\/pangenome\/vcfbub\" id=\"link-26100\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcfbub<\/a>\n<!-- Time to render name section of link id 26100: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Popping bubbles in vg deconstruct VCFs.<\/p>\n<!-- Time to render link large description section of link id 26100: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcfbub> How to use <\/a>\n<!-- Time to render notes section of link id 26100: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26100: 0.00018978118896484 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    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class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/pavanvidem\/blockclust\" id=\"link-24025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BlockClust<\/a>\n<!-- Time to render name section of link id 24025: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BlockClust is an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. BlockClust allows both clustering and classification of small non-coding RNAs.<\/p>\n<!-- Time to render link large description section of link id 24025: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24025: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24025: 0.00011897087097168 --> \n<tr><td><a href=\"http:\/\/bio.cs.washington.edu\/yzizhen\/CMfinder\/\" id=\"link-24182\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CMfinder<\/a>\n<!-- Time to render name section of link id 24182: 1.9073486328125E-6 --> \n<\/td>\n<td><p>CMfinder is a RNA motif prediction tool.<\/p>\n<!-- Time to render link large description section of link id 24182: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24182: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24182: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/spyros-lytras\/dinuq\" id=\"link-24200\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DinuQ<\/a>\n<!-- Time to render name section of link id 24200: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The DinuQ (Dinucleotide Quantification) Python3 package provides a range of metrics for quantifying nucleotide, dinucleotide and synonymous codon representation in genetic sequences.<\/p>\n<!-- Time to render link large description section of link id 24200: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24200: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24200: 0.00011301040649414 --> \n<tr><td><a href=\"http:\/\/emboss.sourceforge.net\/\" id=\"link-23882\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMBOSS<\/a>\n<!-- Time to render name section of link id 23882: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EMBOSS is \"The European Molecular Biology Open Software Suite\". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.<\/p>\n<!-- Time to render link large description section of link id 23882: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMBOSS> How to use <\/a>\n<!-- Time to render notes section of link id 23882: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23882: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/bioinfo.ut.ee\/?page_id=167\" id=\"link-24228\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastaGrep<\/a>\n<!-- Time to render name section of link id 24228: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. It can do both match\/mismatch based and thermodynamic binding energy searches.<\/p>\n<!-- Time to render link large description section of link id 24228: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24228: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24228: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/uni-halle\/gerbil\" id=\"link-24250\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gerbil<\/a>\n<!-- Time to render name section of link id 24250: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A basic task in bioinformatics is the counting of k-mers in genome strings.<\/p>\n<!-- Time to render link large description section of link id 24250: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24250: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24250: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/homer.ucsd.edu\/homer\/\" id=\"link-23643\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Homer<\/a>\n<!-- Time to render name section of link id 23643: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.\u00a0 It is a collection of command line programs for unix-style operating systems written in Perl and C++.<\/p>\n<!-- Time to render link large description section of link id 23643: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HOMER> How to use <\/a>\n<!-- Time to render notes section of link id 23643: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23643: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/Superzchen\/iFeature\" id=\"link-26174\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iFeature<\/a>\n<!-- Time to render name section of link id 26174: 2.1457672119141E-6 --> \n<\/td>\n<td><p>iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. Install with Spann model: https:\/\/github.com\/nicolagulmini\/spaan<\/p>\n<!-- Time to render link large description section of link id 26174: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_iFeature> How to use <\/a>\n<!-- Time to render notes section of link id 26174: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26174: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/ldenti\/kmap\" id=\"link-24338\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmap<\/a>\n<!-- Time to render name section of link id 24338: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Standalone tool based on the bwa index to locate a set of kmers along a reference genome.<\/p>\n<!-- Time to render link large description section of link id 24338: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24338: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24338: 0.00011706352233887 --> \n<tr><td><a href=\"http:\/\/meme-suite.org\/\" id=\"link-23664\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEME<\/a>\n<!-- Time to render name section of link id 23664: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The MEME Suite allows you to: (1)&amp;nbspdiscover motifs using MEME or GLAM2 on groups of related DNA or protein sequences, (2)&amp;nbspsearch sequence databases using motifs, (3)&amp;nbspcompare a motif to all motifs in a database of motifs, and (3)&amp;nbspassociate motifs with Gene Ontology terms via their putative target genes.<\/p>\n<!-- Time to render link large description section of link id 23664: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MEME> How to use <\/a>\n<!-- Time to render notes section of link id 23664: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23664: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/sib-swiss\/pftools3\" id=\"link-23689\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pftools3<\/a>\n<!-- Time to render name section of link id 23689: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases<\/p>\n<!-- Time to render link large description section of link id 23689: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pftools3> How to use <\/a>\n<!-- Time to render notes section of link id 23689: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23689: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/r-loop.org\/?pg=qmrlfs\" id=\"link-24107\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">QmRLFS-finder<\/a>\n<!-- Time to render name section of link id 24107: 1.9073486328125E-6 --> \n<\/td>\n<td><p>QmRLFS-finder, the first R-loop finding tool which uses (unsupervised) QmRLFS (Quantitative Models of RLFS) models to predict RLFSs. This command line tool generates locations and detailed information of RLFSs as well as standards-compliant output files for further analysis and visualization.<\/p>\n<!-- Time to render link large description section of link id 24107: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_QmRLFS-finder> How to use <\/a>\n<!-- Time to render notes section of link id 24107: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24107: 0.00012016296386719 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-leipzig.de\/~kristin\/Software\/RNAclust\/\" id=\"link-24499\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RNAclust<\/a>\n<!-- Time to render name section of link id 24499: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif.<\/p>\n<!-- Time to render link large description section of link id 24499: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24499: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24499: 0.00012898445129395 --> \n<tr><td><a href=\"http:\/\/blog.theseed.org\/servers\/2010\/07\/scan-for-matches.html\" id=\"link-23723\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scan For Matches<\/a>\n<!-- Time to render name section of link id 23723: 3.0994415283203E-6 --> \n<\/td>\n<td><p><b><\/b>scan_for_matches is a utility written in C for locating patterns in DNA or protein FASTA files.<\/p>\n<!-- Time to render link large description section of link id 23723: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23723: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23723: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/CBGR\/jaspar_enrichment\/src\/master\/\" id=\"link-24331\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VAST-TOOLS<\/a>\n<!-- Time to render name section of link id 24331: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Vertebrate Alternative Splicing and Transcription Tools (VAST-TOOLS) is a toolset for profiling and comparing alternative splicing events in RNA-Seq data.<\/p>\n<!-- Time to render link large description section of link id 24331: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24331: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24331: 0.00010895729064941 --> \n\t<\/table>\n<\/div><!-- Div End Category 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class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/fanhuan\/AAF\" id=\"link-24132\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AAF<\/a>\n<!-- Time to render name section of link id 24132: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This is a package for constructing phylogeny without doing alignment or assembly.<\/p>\n<!-- Time to render link large description section of link id 24132: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24132: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24132: 0.00014185905456543 --> \n<tr><td><a href=\"http:\/\/adegenet.r-forge.r-project.org\" id=\"link-24134\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">adegenet<\/a>\n<!-- Time to render name section of link id 24134: 2.8610229492188E-6 --> \n<\/td>\n<td><p>R package dedicated to the exploratory analysis of genetic data. 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Suitable for clustering multiple groups of homologous sequences.\n<!-- Time to render link large description section of link id 25570: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ALFATClust> How to use <\/a>\n<!-- Time to render notes section of link id 25570: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25570: 0.00012898445129395 --> \n<tr><td><a href=\"https:\/\/github.com\/sixthresearcher\/amplisat\" id=\"link-25403\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AmpliSAT<\/a>\n<!-- Time to render name section of link id 25403: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AmpliSAT (Amplicon Sequencing Analysis Tools) are a set of online tools that make easy the analysis of Amplicon Sequencing experiments.<\/p>\n<!-- Time to render link large description section of link id 25403: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AmpliSAT> How to use <\/a>\n<!-- Time to render notes section of link id 25403: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25403: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/anvio.org\/\" id=\"link-23858\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Anvio<\/a>\n<!-- Time to render name section of link id 23858: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Anvi\u2019o is an analysis and visualization platform for \u2018omics data. It brings together many aspects of today\u2019s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs.<\/p>\n<!-- Time to render link large description section of link id 23858: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Anvio> How to use <\/a>\n<!-- Time to render notes section of link id 23858: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23858: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/DominikBuchner\/apscale\" id=\"link-25174\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Apscale<\/a>\n<!-- Time to render name section of link id 25174: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data<\/p>\n<!-- Time to render link large description section of link id 25174: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Apscale> How to use <\/a>\n<!-- Time to render notes section of link id 25174: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25174: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/CshlSiepelLab\/argweaver\/\" id=\"link-26136\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARGweaver<\/a>\n<!-- Time to render name section of link id 26136: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The ARGweaver\/ARGweaver-D software package contains programs and libraries for sampling and manipulating ancestral recombination graphs (ARGs).<\/p>\n<!-- Time to render link large description section of link id 26136: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ARGweaver> How to use <\/a>\n<!-- Time to render notes section of link id 26136: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26136: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/BBaloglu\/ASHURE\" id=\"link-24145\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASHURE<\/a>\n<!-- Time to render name section of link id 24145: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python-based pipeline for analyzing Nanopore sequencing metabarcoding data. ASHURE can take a reference database in order to improve accuracy.<\/p>\n<!-- Time to render link large description section of link id 24145: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24145: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24145: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/chaoszhang\/ASTER\" id=\"link-24147\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASTER<\/a>\n<!-- Time to render name section of link id 24147: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A family of ASTRAL-like algorithms.<\/p>\n<!-- Time to render link large description section of link id 24147: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ASTER> How to use <\/a>\n<!-- Time to render notes section of link id 24147: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24147: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/smirarab\/ASTRAL\" id=\"link-23901\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASTRAL<\/a>\n<!-- Time to render name section of link id 23901: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.<\/p>\n<!-- Time to render link large description section of link id 23901: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ASTRAL> How to use <\/a>\n<!-- Time to render notes section of link id 23901: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23901: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/chaoszhang\/A-pro\" id=\"link-24148\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASTRAL-Pro<\/a>\n<!-- Time to render name section of link id 24148: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ASTRAL-Pro stands for ASTRAL for PaRalogs and Orthologs. ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.<\/p>\n<!-- Time to render link large description section of link id 24148: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24148: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24148: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/oschwengers\/bakta\" id=\"link-24151\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bakta<\/a>\n<!-- Time to render name section of link id 24151: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids.<\/p>\n<!-- Time to render link large description section of link id 24151: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bakta> How to use <\/a>\n<!-- Time to render notes section of link id 24151: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24151: 0.00013017654418945 --> \n<tr><td><a href=\"http:\/\/bali-phy.org\" id=\"link-23974\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BAli-Phy<\/a>\n<!-- Time to render name section of link id 23974: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BAli-Phy is software by Ben Redelings that estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. 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This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.<\/p>\n<!-- Time to render link large description section of link id 24121: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24121: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24121: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/beagle-dev\/beagle-lib\" id=\"link-24016\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle-lib<\/a>\n<!-- Time to render name section of link id 24016: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BEAGLE-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages<\/p>\n<!-- Time to render link large description section of link id 24016: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Beagle-lib> How to use <\/a>\n<!-- Time to render notes section of link id 24016: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24016: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/beast.community\" id=\"link-24130\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BEAST<\/a>\n<!-- Time to render name section of link id 24130: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.<\/p>\r\n<p>BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.<\/p>\n<!-- Time to render link large description section of link id 24130: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BEAST> How to use <\/a>\n<!-- Time to render notes section of link id 24130: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24130: 0.00011110305786133 --> \n<tr><td><a href=\"http:\/\/beast2.org\/\" id=\"link-23805\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BEAST2<\/a>\n<!-- Time to render name section of link id 23805: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.<\/p>\n<!-- Time to render link large description section of link id 23805: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BEAST2> How to use <\/a>\n<!-- Time to render notes section of link id 23805: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23805: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/git.wageningenur.nl\/medema-group\/BiG-SCAPE\" id=\"link-24080\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BIG-SCAPE<\/a>\n<!-- Time to render name section of link id 24080: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Biosynthetic Genes Similarity Clustering and Prospecting Engine. Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency Index)<\/p>\n<!-- Time to render link large description section of link id 24080: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24080: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24080: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/DRL\/blobtools\" id=\"link-24162\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BlobTools<\/a>\n<!-- Time to render name section of link id 24162: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.<\/p>\n<!-- Time to render link large description section of link id 24162: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BlobTools> How to use <\/a>\n<!-- Time to render notes section of link id 24162: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24162: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/DominikBuchner\/BOLDigger\" id=\"link-25005\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BOLDigger<\/a>\n<!-- Time to render name section of link id 25005: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python program to query .fasta files against the different databases of www.boldsystems.org<\/p>\n<!-- Time to render link large description section of link id 25005: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BOLDigger> How to use <\/a>\n<!-- Time to render notes section of link id 25005: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25005: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/BioPP\/bppsuite\" id=\"link-25657\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BppSuite<\/a>\n<!-- Time to render name section of link id 25657: 1.215934753418E-5 --> \n<\/td>\n<td><p>BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.<\/p>\n<!-- Time to render link large description section of link id 25657: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BppSuite> How to use <\/a>\n<!-- Time to render notes section of link id 25657: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25657: 0.00055193901062012 --> \n<tr><td><a href=\"https:\/\/github.com\/jenniferlu717\/Bracken\" id=\"link-23966\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bracken<\/a>\n<!-- Time to render name section of link id 23966: 4.7206878662109E-5 --> \n<\/td>\n<td><p>Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.<\/p>\n<!-- Time to render link large description section of link id 23966: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bracken> How to use <\/a>\n<!-- Time to render notes section of link id 23966: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23966: 0.00039005279541016 --> \n<tr><td><a href=\"http:\/\/www.stat.wisc.edu\/~ane\/bucky\/index.html\" id=\"link-23995\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BUCKy<\/a>\n<!-- Time to render name section of link id 23995: 7.1525573730469E-6 --> \n<\/td>\n<td><p>BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis.<\/p>\n<!-- Time to render link large description section of link id 23995: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23995: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23995: 0.00034308433532715 --> \n<tr><td><a href=\"https:\/\/github.com\/hahnlab\/CAFE5\" id=\"link-24171\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAFE<\/a>\n<!-- Time to render name section of link id 24171: 7.1525573730469E-6 --> \n<\/td>\n<td><p>Software for Computational Analysis of gene Family Evolution. The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences.<\/p>\n<!-- Time to render link large description section of link id 24171: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAFE> How to use <\/a>\n<!-- Time to render notes section of link id 24171: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24171: 0.00033998489379883 --> \n<tr><td><a href=\"https:\/\/github.com\/moshi4\/CafePlotter\" id=\"link-25626\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CafePlotter<\/a>\n<!-- Time to render name section of link id 25626: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A tool for plotting CAFE5 gene family expansion\/contraction result.<\/p>\n<!-- Time to render link large description section of link id 25626: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CafePlotter> How to use <\/a>\n<!-- Time to render notes section of link id 25626: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25626: 0.00052905082702637 --> \n<tr><td><a href=\"https:\/\/github.com\/CAMI-challenge\/AMBER\" id=\"link-24671\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAMI-AMBER<\/a>\n<!-- Time to render name section of link id 24671: 7.1525573730469E-6 --> \n<\/td>\n<td><p>AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets.<\/p>\n<!-- Time to render link large description section of link id 24671: 5.0067901611328E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24671: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24671: 0.00035190582275391 --> \n<tr><td><a href=\"https:\/\/github.com\/EBI-Metagenomics\/emg-viral-pipeline\" id=\"link-25569\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAMISIM<\/a>\n<!-- Time to render name section of link id 25569: 7.1525573730469E-6 --> \n<\/td>\n<td><p>CAMISIM is a software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets.<\/p>\n<!-- Time to render link large description section of link id 25569: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAMISIM> How to use <\/a\n<!-- Time to render notes section of link id 25569: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25569: 0.00033688545227051 --> \n<tr><td><a href=\"https:\/\/github.com\/LouisPwr\/CarpeDeam\" id=\"link-25707\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CarpeDeam<\/a>\n<!-- Time to render name section of link id 25707: 6.9141387939453E-6 --> \n<\/td>\n<td><p>CarpeDeam is a damage-aware metagenome assembler for ancient metagenomic DNA datasets. It takes (merged) reads and a damage matrix as input and prooved to work best for heavily damaged datasets.<\/p>\n<!-- Time to render link large description section of link id 25707: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CarpeDeam> How to use <\/a>\n<!-- Time to render notes section of link id 25707: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25707: 0.00033402442932129 --> \n<tr><td><a href=\"https:\/\/github.com\/vrmarcelino\/CCMetagen\" id=\"link-24115\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CCMetagen<\/a>\n<!-- Time to render name section of link id 24115: 6.9141387939453E-6 --> \n<\/td>\n<td><p>CCMetagen processes sequence alignments produced with KMA, which implements the ConClave sorting scheme to achieve highly accurate read mappings. CCMetagen processes sequence alignments produced with KMA, which implements the ConClave sorting scheme to achieve highly accurate read mappings. CCMetagen produces ranked taxonomic results in user-friendly formats that are ready for publication or downstream statistical analyses.<\/p>\n<!-- Time to render link large description section of link id 24115: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24115: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24115: 0.0003352165222168 --> \n<tr><td><a href=\"http:\/\/ccb.jhu.edu\/software\/centrifuge\/index.shtml\" id=\"link-23871\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Centrifuge<\/a>\n<!-- Time to render name section of link id 23871: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Classifier for metagenomic sequences. Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers.<\/p>\n<!-- Time to render link large description section of link id 23871: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Centrifuge> How to use <\/a>\n<!-- Time to render notes section of link id 23871: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23871: 0.00013518333435059 --> \n<tr><td><a href=\"https:\/\/ecogenomics.github.io\/CheckM\/\" id=\"link-25097\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CheckM<\/a>\n<!-- Time to render name section of link id 25097: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.<\/p>\n<!-- Time to render link large description section of link id 25097: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CheckM> How to use <\/a>\n<!-- Time to render notes section of link id 25097: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25097: 0.00013184547424316 --> \n<tr><td><a href=\"https:\/\/github.com\/chklovski\/CheckM2\" id=\"link-25590\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CheckM2<\/a>\n<!-- Time to render name section of link id 25590: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assessing the quality of metagenome-derived genome bins using machine learning.<\/p>\n<!-- Time to render link large description section of link id 25590: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CheckM2> How to use <\/a>\n<!-- Time to render notes section of link id 25590: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25590: 0.00014209747314453 --> \n<tr><td><a href=\"https:\/\/github.com\/xavierdidelot\/ClonalFrameML\" id=\"link-25352\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClonalFrameML<\/a>\n<!-- Time to render name section of link id 25352: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A software package that performs efficient inference of recombination in bacterial genomes.<\/p>\n<!-- Time to render link large description section of link id 25352: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClonalFrameML> How to use <\/a>\n<!-- Time to render notes section of link id 25352: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25352: 0.00013494491577148 --> \n<tr><td><a href=\"https:\/\/github.com\/ziyewang\/COMEBin\" id=\"link-25576\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">COMEBin<\/a>\n<!-- Time to render name section of link id 25576: 2.1457672119141E-6 --> \n<\/td>\n<td><p>COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning.<\/p>\n<!-- Time to render link large description section of link id 25576: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_COMEBin> How to use <\/a>\n<!-- Time to render notes section of link id 25576: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25576: 0.0001378059387207 --> \n<tr><td><a href=\"https:\/\/github.com\/BinPro\/CONCOCT\" id=\"link-23870\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CONCOCT<\/a>\n<!-- Time to render name section of link id 23870: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.<\/p>\n<!-- Time to render link large description section of link id 23870: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CONCOCT> How to use <\/a>\n<!-- Time to render notes section of link id 23870: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23870: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/github.com\/wwood\/CoverM\" id=\"link-24187\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CoverM<\/a>\n<!-- Time to render name section of link id 24187: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Read coverage calculator for metagenomics.<\/p>\n<!-- Time to render link large description section of link id 24187: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CoverM> How to use <\/a>\n<!-- Time to render notes section of link id 24187: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24187: 0.00022506713867188 --> \n<tr><td><a href=\"https:\/\/github.com\/gjeunen\/reference_database_creator\" id=\"link-25168\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRABS<\/a>\n<!-- Time to render name section of link id 25168: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CRABS (Creating Reference databases for Amplicon-Based Sequencing) is a versatile software program that generates curated reference databases for metagenomic analysis.<\/p>\n<!-- Time to render link large description section of link id 25168: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CRABS> How to use <\/a>\n<!-- Time to render notes section of link id 25168: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25168: 0.00014090538024902 --> \n<tr><td><a href=\"https:\/\/github.com\/kunWangkun\/d2SBin\" id=\"link-23916\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">d2SBin<\/a>\n<!-- Time to render name section of link id 23916: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Improving the binning of metagenomic contigs on d2S oligonucleotide frequency dissimilarity<\/p>\n<!-- Time to render link large description section of link id 23916: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23916: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23916: 0.00013518333435059 --> \n<tr><td><a href=\"https:\/\/github.com\/cmks\/DAS_Tool\" id=\"link-24192\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DAS_Tool<\/a>\n<!-- Time to render name section of link id 24192: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.<\/p>\n<!-- Time to render link large description section of link id 24192: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24192: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24192: 0.0001368522644043 --> \n<tr><td><a href=\"https:\/\/github.com\/MoorjaniLab\/DATES_v4010\" id=\"link-24193\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DATES<\/a>\n<!-- Time to render name section of link id 24193: 1.9073486328125E-6 --> \n<\/td>\n<td><p>DATES (Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Narasimhan, Patterson et al. 2018<\/p>\n<!-- Time to render link large description section of link id 24193: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DATES> How to use <\/a>\n<!-- Time to render notes section of link id 24193: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24193: 0.00013518333435059 --> \n<tr><td><a href=\"https:\/\/github.com\/msettles\/dbcAmplicons\" id=\"link-24194\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dbcAmplicons<\/a>\n<!-- Time to render name section of link id 24194: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Analysis of Double Barcoded Illumina Amplicon Data.<\/p>\n<!-- Time to render link large description section of link id 24194: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24194: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24194: 0.00013494491577148 --> \n<tr><td><a href=\"https:\/\/github.com\/CamilaDuitama\/decOM\" id=\"link-25231\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">decOM<\/a>\n<!-- Time to render name section of link id 25231: 2.1457672119141E-6 --> \n<\/td>\n<td><p>decOM is a high-accuracy microbial source tracking method that is suitable for contamination quantification in paleogenomics, namely the analysis of collections of possibly contaminated ancient oral metagenomic data sets.<\/p>\n<!-- Time to render link large description section of link id 25231: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_decOM> How to use <\/a>\n<!-- Time to render notes section of link id 25231: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25231: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/champost\/DECX\" id=\"link-24082\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DECX<\/a>\n<!-- Time to render name section of link id 24082: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This is the DECX (DEC eXtended) model for historical biogeographic inference<\/p>\n<!-- Time to render link large description section of link id 24082: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24082: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24082: 0.00014495849609375 --> \n<tr><td><a href=\"https:\/\/github.com\/chrisquince\/DESMAN\" id=\"link-23869\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DESMAN<\/a>\n<!-- Time to render name section of link id 23869: 1.9073486328125E-6 --> \n<\/td>\n<td><p>De novo Extraction of Strains from MetAgeNomes.<\/p>\n<!-- Time to render link large description section of link id 23869: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23869: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23869: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/github.com\/lgueguen\/DGINN\" id=\"link-25664\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DGINN<\/a>\n<!-- Time to render name section of link id 25664: 3.814697265625E-6 --> \n<\/td>\n<td><p>DGINN is a pipeline dedicated to the detection of genetic innovations, starting from a gene sequence.<\/p>\n<!-- Time to render link large description section of link id 25664: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DGINN> How to use <\/a>\n<!-- Time to render notes section of link id 25664: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25664: 0.00023698806762695 --> \n<tr><td><a href=\"https:\/\/www.cs.hmc.edu\/~yjw\/software\/dlcpar\/\" id=\"link-23820\" class=\"track_this_link \" rel=\"noopener noreferrer\">DLCpar<\/a>\n<!-- Time to render name section of link id 23820: 2.8610229492188E-6 --> \n<\/td>\n<td><p>DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).<\/p>\n<!-- Time to render link large description section of link id 23820: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DLCpar> How to use <\/a>\n<!-- Time to render notes section of link id 23820: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23820: 0.00013995170593262 --> \n<tr><td><a href=\"https:\/\/github.com\/vuthuyduong\/dnabarcoder\" id=\"link-26086\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dnabarcoder<\/a>\n<!-- Time to render name section of link id 26086: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Dnabarcoder is a tool to PREDICT global and local similarity cut-offs for fungal sequence identification for a reference dataset, and CLASSIFY unidentified sequences based on the predicted similarity cutoffs.<\/p>\n<!-- Time to render link large description section of link id 26086: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dnabarcoder> How to use <\/a>\n<!-- Time to render notes section of link id 26086: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26086: 0.00021195411682129 --> \n<tr><td><a href=\"https:\/\/github.com\/shafferm\/DRAM\" id=\"link-24202\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DRAM<\/a>\n<!-- Time to render name section of link id 24202: 2.1457672119141E-6 --> \n<\/td>\n<td><p>DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs.<\/p>\n<!-- Time to render link large description section of link id 24202: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24202: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24202: 0.00014114379882812 --> \n<tr><td><a href=\"http:\/\/egglib.sourceforge.net\" id=\"link-23618\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EggLib<\/a>\n<!-- Time to render name section of link id 23618: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EggLib is a C++\/Python library and program package for evolutionary genetics and genomics.<\/p>\n<!-- Time to render link large description section of link id 23618: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23618: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23618: 0.00013589859008789 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/g.hmc.edu\/empress\/home\" id=\"link-24212\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eMPRess<\/a>\n<!-- Time to render name section of link id 24212: 3.0994415283203E-6 --> \n<\/td>\n<td><p>eMPRess is a software tool for reconciling pairs of phylogenetic trees such as host-parasite, host-symbiont, and species-gene trees under the Duplication-Transfer-Loss (DTL) model.<\/p>\n<!-- Time to render link large description section of link id 24212: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eMPRess> How to use <\/a>\n<!-- Time to render notes section of link id 24212: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24212: 0.00022077560424805 --> \n<tr><td><a href=\"https:\/\/github.com\/treangenlab\/emu\" id=\"link-25417\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Emu<\/a>\n<!-- Time to render name section of link id 25417: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Emu is a relative abundance estimator for 16S genomic sequences. The method is optimized for error-prone full-length reads, but can also be utilized for short-read data.<\/p>\n<!-- Time to render link large description section of link id 25417: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Emu> How to use <\/a>\n<!-- Time to render notes section of link id 25417: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25417: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/phylo42\/EPIK\" id=\"link-25431\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EPIK<\/a>\n<!-- Time to render name section of link id 25431: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EPIK is a program for rapid alignment-free phylogenetic placement.<\/p>\n<!-- Time to render link large description section of link id 25431: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EPIK> How to use <\/a>\n<!-- Time to render notes section of link id 25431: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25431: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/etetoolkit\/ete\" id=\"link-24085\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ETE<\/a>\n<!-- Time to render name section of link id 24085: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Python framework for the analysis and visualization of trees.<\/p>\n<!-- Time to render link large description section of link id 24085: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.11.1 and <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ETE> How to use <\/a>\n<!-- Time to render notes section of link id 24085: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24085: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/Finn-Lab\/EukCC\" id=\"link-24218\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EukCC<\/a>\n<!-- Time to render name section of link id 24218: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.<\/p>\n<!-- Time to render link large description section of link id 24218: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24218: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24218: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/patrickwest\/EukRep\" id=\"link-24219\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EukRep<\/a>\n<!-- Time to render name section of link id 24219: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets.<\/p>\n<!-- Time to render link large description section of link id 24219: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EukRep> How to use <\/a>\n<!-- Time to render notes section of link id 24219: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24219: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/cme.h-its.org\/exelixis\/web\/software\/exabayes\/index.html\" id=\"link-24221\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Exabayes<\/a>\n<!-- Time to render name section of link id 24221: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.<\/p>\n<!-- Time to render link large description section of link id 24221: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24221: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24221: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/stamatak\/ExaML\" id=\"link-23620\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ExaML<\/a>\n<!-- Time to render name section of link id 23620: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI.<\/p>\n<!-- Time to render link large description section of link id 23620: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ExaML> How to use <\/a>\n<!-- Time to render notes section of link id 23620: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23620: 0.00011491775512695 --> \n<tr><td><a href=\"http:\/\/www.atgc-montpellier.fr\/fastme\/\" id=\"link-23819\" class=\"track_this_link \" rel=\"noopener noreferrer\">FastME<\/a>\n<!-- Time to render name section of link id 23819: 2.1457672119141E-6 --> \n<\/td>\n<td><p>FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of NJ. FastME improves over NJ by performing topological moves using fast, sophisticated algorithms.<\/p>\n<!-- Time to render link large description section of link id 23819: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastME> How to use <\/a>\n<!-- Time to render notes section of link id 23819: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23819: 0.00011110305786133 --> \n<tr><td><a href=\"http:\/\/www.microbesonline.org\/fasttree\/\" id=\"link-23774\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastTree<\/a>\n<!-- Time to render name section of link id 23774: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.<\/p>\n<!-- Time to render link large description section of link id 23774: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastTree> How to use <\/a>\n<!-- Time to render notes section of link id 23774: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23774: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/rambaut\/figtree\" id=\"link-25257\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FigTree<\/a>\n<!-- Time to render name section of link id 25257: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.<\/p>\n<!-- Time to render link large description section of link id 25257: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FigTree> How to use <\/a>\n<!-- Time to render notes section of link id 25257: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25257: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/frogs.toulouse.inra.fr\" id=\"link-24240\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FROGS<\/a>\n<!-- Time to render name section of link id 24240: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FROGS is a CLI workflow designed to produce an OTU count matrix from high depth sequencing amplicon data.<\/p>\n<!-- Time to render link large description section of link id 24240: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FROGS> How to use <\/a>\n<!-- Time to render notes section of link id 24240: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24240: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/gphocs-dev\/G-PhoCS\" id=\"link-25558\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">G-PhoCS<\/a>\n<!-- Time to render name section of link id 25558: 1.9073486328125E-6 --> \n<\/td>\n<td>G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.\n<!-- Time to render link large description section of link id 25558: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_G-PhoCS> How to use <\/a>\n<!-- Time to render notes section of link id 25558: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25558: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/pirovc\/ganon\" id=\"link-24855\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ganon<\/a>\n<!-- Time to render name section of link id 24855: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ganon classifies DNA sequences against large sets of genomic reference sequences efficiently.<\/p>\n<!-- Time to render link large description section of link id 24855: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24855: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24855: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/lczech\/gappa\" id=\"link-25572\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gappa<\/a>\n<!-- Time to render name section of link id 25572: 1.9073486328125E-6 --> \n<\/td>\n<td>A toolkit for analyzing and visualizing phylogenetic (placement) data.\n<!-- Time to render link large description section of link id 25572: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gappa> How to use <\/a>\n<!-- Time to render notes section of link id 25572: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25572: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/zwickl\/garli\" id=\"link-24091\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GARLI<\/a>\n<!-- Time to render name section of link id 24091: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees.<\/p>\n<!-- Time to render link large description section of link id 24091: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24091: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24091: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks.html\" id=\"link-23765\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gblocks<\/a>\n<!-- Time to render name section of link id 23765: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. These positions may not be homologous or may have been saturated by multiple substitutions and it is convenient to eliminate them prior to phylogenetic analysis.<\/p>\n<!-- Time to render link large description section of link id 23765: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gblocks> How to use <\/a>\n<!-- Time to render notes section of link id 23765: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23765: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/evolbioinfo\/gotree\" id=\"link-25525\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gotree<\/a>\n<!-- Time to render name section of link id 25525: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Gotree is a set of command line tools and an API to manipulate phylogenetic trees.<\/p>\n<!-- Time to render link large description section of link id 25525: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gotree> How to use <\/a>\n<!-- Time to render notes section of link id 25525: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25525: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/achtman-lab\/GrapeTree\" id=\"link-24260\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">GrapeTree<\/a>\n<!-- Time to render name section of link id 24260: 5.0067901611328E-6 --> \n<\/td>\n<td><p>GrapeTree is a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.<\/p>\n<!-- Time to render link large description section of link id 24260: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GrapeTree> How to use <\/a>\n<!-- Time to render notes section of link id 24260: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24260: 0.00044989585876465 --> \n<tr><td><a href=\"http:\/\/huttenhower.sph.harvard.edu\/GraPhlAn\" id=\"link-23837\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraPhlAn<\/a>\n<!-- Time to render name section of link id 23837: 3.814697265625E-6 --> \n<\/td>\n<td><p>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.<\/p>\n<!-- Time to render link large description section of link id 23837: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23837: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23837: 0.0002288818359375 --> \n<tr><td><a href=\"https:\/\/ecogenomics.github.io\/GTDBTk\/\" id=\"link-24266\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GTDB-Tk<\/a>\n<!-- Time to render name section of link id 24266: 5.0067901611328E-6 --> \n<\/td>\n<td><p>GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.<\/p>\n<!-- Time to render link large description section of link id 24266: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GTDB-Tk> How to use <\/a>\n<!-- Time to render notes section of link id 24266: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24266: 0.00028300285339355 --> \n<tr><td><a href=\"https:\/\/github.com\/nickjcroucher\/gubbins\" id=\"link-24268\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gubbins<\/a>\n<!-- Time to render name section of link id 24268: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.<\/p>\n<!-- Time to render link large description section of link id 24268: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gubbins> How to use <\/a>\n<!-- Time to render notes section of link id 24268: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24268: 0.00035405158996582 --> \n<tr><td><a href=\"https:\/\/forge-dga.jouy.inra.fr\/projects\/hapflk\/\" id=\"link-23640\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hapflk<\/a>\n<!-- Time to render name section of link id 23640: 4.0531158447266E-6 --> \n<\/td>\n<td><p>hapflk is a software implementing the hapFLK <1> and FLK <2> tests for the detection of selection signatures based on multiple population genotyping data.<\/p>\n<!-- Time to render link large description section of link id 23640: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hapflk> How to use <\/a>\n<!-- Time to render notes section of link id 23640: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23640: 0.00025510787963867 --> \n<tr><td><a href=\"https:\/\/github.com\/gwcbi\/haphpipe\" id=\"link-25171\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HAPHPIPE<\/a>\n<!-- Time to render name section of link id 25171: 4.0531158447266E-6 --> \n<\/td>\n<td><p>NGS viral assembly and population genetics.<\/p>\n<!-- Time to render link large description section of link id 25171: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HAPHPIPE> How to use <\/a>\n<!-- Time to render notes section of link id 25171: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25171: 0.00023102760314941 --> \n<tr><td><a href=\"https:\/\/github.com\/xfengnefx\/hifiasm-meta\" id=\"link-24293\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\">hifiasm-meta<\/a>\n<!-- Time to render name section of link id 24293: 4.0531158447266E-6 --> \n<\/td>\n<td><p>De novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.<\/p>\n<!-- Time to render link large description section of link id 24293: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hifiasm-meta> How to use <\/a>\n<!-- Time to render notes section of link id 24293: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24293: 0.00022411346435547 --> \n<tr><td><a href=\"https:\/\/hyphy.org\/\" id=\"link-23645\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HyPhy<\/a>\n<!-- Time to render name section of link id 23645: 4.0531158447266E-6 --> \n<\/td>\n<td><p>HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses.<\/p>\n<!-- Time to render link large description section of link id 23645: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HyPhy> How to use <\/a>\n<!-- Time to render notes section of link id 23645: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23645: 0.00023794174194336 --> \n<tr><td><a href=\"https:\/\/github.com\/HadrienG\/InSilicoSeq\" id=\"link-25786\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">InSilicoSeq<\/a>\n<!-- Time to render name section of link id 25786: 6.9141387939453E-6 --> \n<\/td>\n<td><p>InSilicoSeq is a sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.<\/p>\n<!-- Time to render link large description section of link id 25786: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_InSilicoSeq> How to use <\/a>\n<!-- Time to render notes section of link id 25786: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25786: 0.00029397010803223 --> \n<tr><td><a href=\"https:\/\/github.com\/phylo42\/IPK\" id=\"link-25430\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IPK<\/a>\n<!-- Time to render name section of link id 25430: 4.0531158447266E-6 --> \n<\/td>\n<td><p>IPK is a tool for computing phylo-k-mers for a fixed phylogeny.<\/p>\n<!-- Time to render link large description section of link id 25430: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IPK> How to use <\/a>\n<!-- Time to render notes section of link id 25430: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25430: 0.00018906593322754 --> \n<tr><td><a href=\"http:\/\/www.iqtree.org\/\" id=\"link-23860\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IQ-TREE<\/a>\n<!-- Time to render name section of link id 23860: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Efficient phylogenomic software by maximum likelihood<\/p>\n<!-- Time to render link large description section of link id 23860: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IQ-TREE> How to use <\/a>\n<!-- Time to render notes section of link id 23860: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23860: 0.00027894973754883 --> \n<tr><td><a href=\"http:\/\/microbiology.se\/software\/itsx\/\" id=\"link-23650\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ITSx<\/a>\n<!-- Time to render name section of link id 23650: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing<\/p>\n<!-- Time to render link large description section of link id 23650: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ITSx> How to use <\/a>\n<!-- Time to render notes section of link id 23650: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23650: 0.00024509429931641 --> \n<tr><td><a href=\"https:\/\/github.com\/andersen-lab\/ivar\" id=\"link-25121\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iVar<\/a>\n<!-- Time to render name section of link id 25121: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Var is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions\/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.<\/p>\n<!-- Time to render link large description section of link id 25121: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_iVar> How to use <\/a>\n<!-- Time to render notes section of link id 25121: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25121: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/code.google.com\/p\/jmodeltest2\/\" id=\"link-23651\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">jModeltest<\/a>\n<!-- Time to render name section of link id 23651: 5.9604644775391E-6 --> \n<\/td>\n<td><p><strong>jModelTest<\/strong> is a tool to carry out statistical selection of best-fit models of nucleotide substitution.<\/p>\n<!-- Time to render link large description section of link id 23651: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23651: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23651: 0.00034213066101074 --> \n<tr><td><a href=\"http:\/\/jphmm.gobics.de\/jphmm.html\" id=\"link-25985\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">jpHMM<\/a>\n<!-- Time to render name section of link id 25985: 4.0531158447266E-6 --> \n<\/td>\n<td><p>jpHMM (jumping profile Hidden Markov Model) is a probabilistic approach to compare a sequence to a multiple alignment of a sequence family. The jpHMM web server at GOBICS is a tool for the detection of recombinations in\u00a0<a href=\"http:\/\/jphmm.gobics.de\/submission_hiv\">HIV-1<\/a>\u00a0and\u00a0<a href=\"http:\/\/jphmm.gobics.de\/submission_hbv\">hepatitis B virus (HBV)<\/a> genomes.<br \/>\r\nFor a query sequence phylogenetic recombination breakpoints are predicted and each region of the sequence is assigned to one HIV-1 subtype\/HBV genotype. This prediction is based on a pre-calculated multiple alignment of the major HIV-1 subtypes\/HBV genotypes. A detailed description of the algorithm and some information about the evaluation can be found\u00a0<a href=\"http:\/\/jphmm.gobics.de\/method.html\">here<\/a>. For information about the output format please see the\u00a0<a href=\"http:\/\/jphmm.gobics.de\/submission\">online submission<\/a>\u00a0page.<\/p>\n<!-- Time to render link large description section of link id 25985: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_jpHMM> How to use <\/a>\n<!-- Time to render notes section of link id 25985: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25985: 0.00020098686218262 --> \n<tr><td><a href=\"https:\/\/github.com\/ridgelab\/JustOrthologs\" id=\"link-23976\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JustOrthologs<\/a>\n<!-- Time to render name section of link id 23976: 5.0067901611328E-6 --> \n<\/td>\n<td><p>A Fast, Accurate, and User-Friendly Ortholog-Finding Algorithm<\/p>\n<!-- Time to render link large description section of link id 23976: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23976: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23976: 0.00028800964355469 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinformatics-centre\/kaiju\" id=\"link-23804\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Kaiju<\/a>\n<!-- Time to render name section of link id 23804: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Fast taxonomic classification of metagenomic sequencing reads using a protein reference database<\/p>\n<!-- Time to render link large description section of link id 23804: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Kaiju> How to use <\/a>\n<!-- Time to render notes section of link id 23804: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23804: 0.0001990795135498 --> \n<tr><td><a href=\"http:\/\/ccb.jhu.edu\/software\/kraken\/\" id=\"link-23908\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Kraken<\/a>\n<!-- Time to render name section of link id 23908: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.<\/p>\n<!-- Time to render link large description section of link id 23908: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23908: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23908: 0.0001218318939209 --> \n<tr><td><a href=\"https:\/\/github.com\/DerrickWood\/kraken2\" id=\"link-24053\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Kraken2<\/a>\n<!-- Time to render name section of link id 24053: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.<\/p>\n<!-- Time to render link large description section of link id 24053: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Kraken2> How to use <\/a>\n<!-- Time to render notes section of link id 24053: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24053: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/jenniferlu717\/KrakenTools\" id=\"link-25601\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KrakenTools<\/a>\n<!-- Time to render name section of link id 25601: 2.8610229492188E-6 --> \n<\/td>\n<td><p>KrakenTools provides individual scripts to analyze Kraken\/Kraken2\/Bracken\/KrakenUniq output files.<\/p>\n<!-- Time to render link large description section of link id 25601: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KrakenTools> How to use <\/a>\n<!-- Time to render notes section of link id 25601: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25601: 0.00020384788513184 --> \n<tr><td><a href=\"https:\/\/github.com\/fbreitwieser\/krakenuniq\" id=\"link-24119\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KrakenUniq<\/a>\n<!-- Time to render name section of link id 24119: 3.814697265625E-6 --> \n<\/td>\n<td><p>KrakenUniq (formerly KrakenHLL) is a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset.<\/p>\n<!-- Time to render link large description section of link id 24119: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KrakenUniq> How to use <\/a>\n<!-- Time to render notes section of link id 24119: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24119: 0.00015091896057129 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/ksnp\/\" id=\"link-25283\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kSNP4<\/a>\n<!-- Time to render name section of link id 25283: 1.9073486328125E-6 --> \n<\/td>\n<td><p>kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.<\/p>\n<!-- Time to render link large description section of link id 25283: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kSNP4> How to use <\/a>\n<!-- Time to render notes section of link id 25283: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25283: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/nsegata\/lefse\" id=\"link-23940\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LEfSe<\/a>\n<!-- Time to render name section of link id 23940: 1.9073486328125E-6 --> \n<\/td>\n<td><p>LEfSe (Linear discriminant analysis effect size) is a tool developed by the Huttenhower group to find biomarkers between 2 or more groups using relative abundances.<\/p>\n<!-- Time to render link large description section of link id 23940: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LEfSe> How to use <\/a>\n<!-- Time to render notes section of link id 23940: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23940: 0.0001671314239502 --> \n<tr><td><a href=\"https:\/\/github.com\/carlosj-rr\/LSx\" id=\"link-25040\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LSx<\/a>\n<!-- Time to render name section of link id 25040: 2.8610229492188E-6 --> \n<\/td>\n<td><p>LS<sup>X<\/sup>\u00a0is a script in R that runs the LS\u00b3 and LS\u2074 algorithms of data subsampling for multigene phylogenetic inference. Both of these algorithms do a gene-by-gene inspection of the heterogeneity of evolutionary rates among user-defined lineages of interest (LOI). Then, using criteria that differ in both algorithms (see details\u00a0<a href=\"https:\/\/github.com\/carlosj-rr\/LSx\/wiki\/Introduction#is-lsx-for-me\">here<\/a>\u00a0or in the\u00a0<a href=\"https:\/\/github.com\/carlosj-rr\/LSx\/wiki\/Citations\">papers<\/a>), they try to find a subsample of sequences that evolve at a homogeneous rate across all LOIs. If this subset is found, an alignment of the gene is produced with only the sequences that evolve homogeneously. At the same time, a table is also produced showing which sequences were \u201cflagged\u201d (the sequences that were removed), and which sequences were kept. If a subset of sequences that evolve at a homogeneous rate is not found, the gene is flagged entirely.<\/p>\n<!-- Time to render link large description section of link id 25040: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LSx> How to use <\/a>\n<!-- Time to render notes section of link id 25040: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25040: 0.0001220703125 --> \n<tr><td><a href=\"http:\/\/ab.inf.uni-tuebingen.de\/software\/malt\/\" id=\"link-24057\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MALT<\/a>\n<!-- Time to render name section of link id 24057: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MALT (MEGAN alignment tool) is an extension of MEGAN (metagenome analyzer).<br \/>\r\nMALT performs alignment of metagenomic reads against a database of reference sequences (such as NR, GenBank or Silva) and produces a MEGAN RMA file as output. The software is currently under development.<\/p>\n<!-- Time to render link large description section of link id 24057: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MALT> How to use <\/a>\n<!-- Time to render notes section of link id 24057: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24057: 0.0001380443572998 --> \n<tr><td><a href=\"https:\/\/github.com\/LaboratorioBioinformatica\/MARVEL\" id=\"link-24366\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MARVEL_bins<\/a>\n<!-- Time to render name section of link id 24366: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MARVEL (Metagenomic Analysis and Retrieval of Viral Elements) is a tool for recovery of draft phage genomes from whole community shotgun metagenomic sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24366: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24366: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24366: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/lskatz\/mashtree\" id=\"link-24993\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mashtree<\/a>\n<!-- Time to render name section of link id 24993: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Create a tree using Mash distances.<\/p>\n<!-- Time to render link large description section of link id 24993: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mashtree> How to use <\/a>\n<!-- Time to render notes section of link id 24993: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24993: 0.00011777877807617 --> \n<tr><td><a href=\"https:\/\/downloads.jbei.org\/data\/microbial_communities\/MaxBin\/MaxBin.html\" id=\"link-23861\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MaxBin2<\/a>\n<!-- Time to render name section of link id 23861: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.<\/p>\n<!-- Time to render link large description section of link id 23861: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23861: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23861: 0.00013017654418945 --> \n<tr><td><a href=\"https:\/\/github.com\/voutcn\/megahit\" id=\"link-23780\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEGAHIT<\/a>\n<!-- Time to render name section of link id 23780: 4.0531158447266E-6 --> \n<\/td>\n<td><p>An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph<\/p>\n<!-- Time to render link large description section of link id 23780: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MEGAHIT> How to use <\/a>\n<!-- Time to render notes section of link id 23780: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23780: 0.00018882751464844 --> \n<tr><td><a href=\"http:\/\/www-ab.informatik.uni-tuebingen.de\/software\/megan\/welcome.html\" id=\"link-23663\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MEGAN<\/a>\n<!-- Time to render name section of link id 23663: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MEtaGenome ANalyzer : Metagenomic data analysis : taxonomic and functionnal (SEED and KEGG classification) analysis.\u00a0<\/p>\n<!-- Time to render link large description section of link id 23663: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MEGAN> How to use <\/a>\n<!-- Time to render notes section of link id 23663: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23663: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/berkeleylab\/metabat\/src\/master\/\" id=\"link-24374\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaBat<\/a>\n<!-- Time to render name section of link id 24374: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24374: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24374: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24374: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/github.com\/envmetagen\/metabinkit\" id=\"link-25994\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">metabinkit<\/a>\n<!-- Time to render name section of link id 25994: 1.9073486328125E-6 --> \n<\/td>\n<td><p>From metagenomic or metabarcoding data, it is often necessary to assign taxonomy to DNA sequences. This is generally performed by aligning sequences to a reference database, usually resulting in multiple database alignments for each query sequence. Using these alignment results, metabinkit assigns a single taxon to each query sequence, based on user-defined percentage identity thresholds. In essence, for each query, the alignments are filtered based on the percentage identity thresholds and the lowest common ancestor for all alignments passing the filters is determined. The metabin program is not limited to BLAST alignments, and can accept alignment results produced using any program, provided the input format is correct. However, functionality is also available to create BLAST databases and to perform BLAST alignments, which can be passed directly to metabin.<\/p>\n<!-- Time to render link large description section of link id 25994: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_metabinkit> How to use <\/a>\n<!-- Time to render notes section of link id 25994: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25994: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/Glouvel\/metabit\" id=\"link-23941\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">metaBIT<\/a>\n<!-- Time to render name section of link id 23941: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.<\/p>\n<!-- Time to render link large description section of link id 23941: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_metaBIT> How to use <\/a>\n<!-- Time to render notes section of link id 23941: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23941: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/metaDMG-dev\/metaDMG-core\" id=\"link-25336\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">metaDMG<\/a>\n<!-- Time to render name section of link id 25336: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and accurate ancient DNA damage toolkit for metagenomic data.<\/p>\n<!-- Time to render link large description section of link id 25336: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_metaDMG> How to use <\/a>\n<!-- Time to render notes section of link id 25336: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25336: 0.00015497207641602 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/metaeuk\" id=\"link-24375\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaEuk<\/a>\n<!-- Time to render name section of link id 24375: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.<\/p>\n<!-- Time to render link large description section of link id 24375: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaEuk> How to use <\/a>\n<!-- Time to render notes section of link id 24375: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24375: 0.0001220703125 --> \n<tr><td><a href=\"http:\/\/csg.sph.umich.edu\/abecasis\/metal\/index.html\" id=\"link-23994\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">METAL<\/a>\n<!-- Time to render name section of link id 23994: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.<\/p>\n<!-- Time to render link large description section of link id 23994: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23994: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23994: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/GaetanBenoitDev\/metaMDBG\" id=\"link-25473\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaMDBG<\/a>\n<!-- Time to render name section of link id 25473: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A lightweight assembler for long and accurate metagenomics reads.<\/p>\n<!-- Time to render link large description section of link id 25473: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaMDBG> How to use <\/a>\n<!-- Time to render notes section of link id 25473: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25473: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/github.com\/biobakery\/MetaPhlAn\" id=\"link-24798\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn<\/a>\n<!-- Time to render name section of link id 24798: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24798: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaPhlAn> How to use <\/a>\n<!-- Time to render notes section of link id 24798: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24798: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/biobakery\/metaphlan\" id=\"link-23665\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn2<\/a>\n<!-- Time to render name section of link id 23665: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MetaPhlAn2 is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.<\/p>\n<!-- Time to render link large description section of link id 23665: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaPhlAn> How to use <\/a>\n<!-- Time to render notes section of link id 23665: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23665: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/biobakery\/MetaPhlAn\/tree\/3.0\" id=\"link-24376\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn3<\/a>\n<!-- Time to render name section of link id 24376: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.<\/p>\n<!-- Time to render link large description section of link id 24376: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24376: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24376: 0.00015020370483398 --> \n<tr><td><a href=\"https:\/\/huttenhower.sph.harvard.edu\/metaphlan\/\" id=\"link-25176\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaPhlAn4<\/a>\n<!-- Time to render name section of link id 25176: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling.<\/p>\n<!-- Time to render link large description section of link id 25176: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaPhlAn> How to use <\/a>\n<!-- Time to render notes section of link id 25176: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25176: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/bxlab\/metaWRAP\" id=\"link-24377\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaWRAP<\/a>\n<!-- Time to render name section of link id 24377: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A flexible pipeline for genome-resolved metagenomic data analysis.<\/p>\n<!-- Time to render link large description section of link id 24377: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MetaWRAP> How to use <\/a>\n<!-- Time to render notes section of link id 24377: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24377: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/microbiology.se\/software\/metaxa2\/\" id=\"link-24378\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Metaxa2<\/a>\n<!-- Time to render name section of link id 24378: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.<\/p>\n<!-- Time to render link large description section of link id 24378: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Metaxa2> How to use <\/a>\n<!-- Time to render notes section of link id 24378: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24378: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/metagenopolis\/meteor\" id=\"link-24891\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">meteor<\/a>\n<!-- Time to render name section of link id 24891: 7.8678131103516E-6 --> \n<\/td>\n<td><p>Meteor (Metagenomic Explorator), a software for profiling metagenomic data at gene level.<\/p>\n<!-- Time to render link large description section of link id 24891: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_meteor> How to use <\/a>\n<!-- Time to render notes section of link id 24891: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24891: 0.00056815147399902 --> \n<tr><td><a href=\"https:\/\/peterbeerli.com\/migrate-html5\/index.html\" id=\"link-25550\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Migrate<\/a>\n<!-- Time to render name section of link id 25550: 7.1525573730469E-6 --> \n<\/td>\n<td>Migrate estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture.\n<!-- Time to render link large description section of link id 25550: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Migrate> How to use <\/a>\n<!-- Time to render notes section of link id 25550: 2.0027160644531E-5 --> \n<\/td><\/tr>\n<!-- Time to render link id 25550: 0.0003659725189209 --> \n<tr><td><a href=\"https:\/\/github.com\/thh32\/MiMiC2\" id=\"link-26236\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiMiC2<\/a>\n<!-- Time to render name section of link id 26236: 5.9604644775391E-6 --> \n<\/td>\n<td><p>MiMiC2 is a bioinformatic pipeline for the selection of a few microbial genomes that functionally represent an entire ecosystem, termed a synthetic community (SynCom).<\/p>\n<!-- Time to render link large description section of link id 26236: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MiMiC2> How to use <\/a>\n<!-- Time to render notes section of link id 26236: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26236: 0.0003511905670166 --> \n<tr><td><a href=\"https:\/\/github.com\/ddarriba\/modeltest\" id=\"link-24001\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ModelTest-NG<\/a>\n<!-- Time to render name section of link id 24001: 6.9141387939453E-6 --> \n<\/td>\n<td><p>ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.<\/p>\n<!-- Time to render link large description section of link id 24001: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ModelTest-NG> How to use <\/a>\n<!-- Time to render notes section of link id 24001: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24001: 0.00035285949707031 --> \n<tr><td><a href=\"http:\/\/www.mothur.org\/wiki\/Main_Page\" id=\"link-23671\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mothur<\/a>\n<!-- Time to render name section of link id 23671: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The one-stop source for your computational microbial ecology needs. mothur offers the ability to go from raw sequences to the generation of visualization tools to describe alpha and beta diversity.<\/p>\n<!-- Time to render link large description section of link id 23671: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mothur> How to use <\/a>\n<!-- Time to render notes section of link id 23671: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23671: 0.00035500526428223 --> \n<tr><td><a href=\"https:\/\/github.com\/Pas-Kapli\/mptp\" id=\"link-24397\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mPTP<\/a>\n<!-- Time to render name section of link id 24397: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A tool for single-locus species delimitation.<\/p>\n<!-- Time to render link large description section of link id 24397: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mPTP> How to use <\/a>\n<!-- Time to render notes section of link id 24397: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24397: 0.00033402442932129 --> \n<tr><td><a href=\"http:\/\/mrbayes.sourceforge.net\/\" id=\"link-23672\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MrBayes<\/a>\n<!-- Time to render name section of link id 23672: 5.9604644775391E-6 --> \n<\/td>\n<td><p>MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.<\/p>\n<!-- Time to render link large description section of link id 23672: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MrBayes> How to use <\/a>\n<!-- Time to render notes section of link id 23672: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23672: 0.00033307075500488 --> \n<tr><td><a href=\"https:\/\/github.com\/arumugamlab\/msamtools\" id=\"link-26027\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msamtools<\/a>\n<!-- Time to render name section of link id 26027: 5.9604644775391E-6 --> \n<\/td>\n<td><p>msamtools provides useful functions that are commonly used in microbiome data analysis, especially when analyzing shotgun metagenomics or metatranscriptomics data.<\/p>\n<!-- Time to render link large description section of link id 26027: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msamtools> How to use <\/a>\n<!-- Time to render notes section of link id 26027: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26027: 0.00023508071899414 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/ccoclet\/mvp\" id=\"link-25282\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MVP<\/a>\n<!-- Time to render name section of link id 25282: 4.0531158447266E-6 --> \n<\/td>\n<td><p>MVP stands for Multi-choice Viromics Pipeline. It is a simplified pipeline that utilizes a suite of state-of-art tools to easily get from a set of contigs to a vOTU heatmap (and more).<\/p>\n<!-- Time to render link large description section of link id 25282: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MVP> How to use <\/a>\n<!-- Time to render notes section of link id 25282: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25282: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/sb2nhri\/files\/MyCC\/\" id=\"link-23915\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MyCC<\/a>\n<!-- Time to render name section of link id 23915: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.<\/p>\n<!-- Time to render link large description section of link id 23915: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23915: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23915: 0.00017905235290527 --> \n<tr><td><a href=\"https:\/\/github.com\/bluenote-1577\/myloasm\" id=\"link-25993\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">myloasm<\/a>\n<!-- Time to render name section of link id 25993: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Myloasm is a de novo metagenome assembler for long-read sequencing data. It takes sequencing reads and outputs polished contigs in a single command.<\/p>\n<!-- Time to render link large description section of link id 25993: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_myloasm> How to use <\/a>\n<!-- Time to render notes section of link id 25993: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25993: 0.00018692016601562 --> \n<tr><td><a href=\"https:\/\/github.com\/ImagoXV\/NanoASV\/tree\/main\" id=\"link-25782\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoASV<\/a>\n<!-- Time to render name section of link id 25782: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Nanopore full-length 16S metabarcoding amplicon data analysis<\/p>\n<!-- Time to render link large description section of link id 25782: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoASV> How to use <\/a>\n<!-- Time to render notes section of link id 25782: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25782: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/genomicsITER\/NanoCLUST\" id=\"link-24407\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCLUST<\/a>\n<!-- Time to render name section of link id 24407: 4.0531158447266E-6 --> \n<\/td>\n<td><p>NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads.<\/p>\n<!-- Time to render link large description section of link id 24407: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoCLUST> How to use <\/a>\n<!-- Time to render notes section of link id 24407: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24407: 0.00018501281738281 --> \n<tr><td><a href=\"http:\/\/cegg.unige.ch\/newick_utils\" id=\"link-24083\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Newick_Utilities<\/a>\n<!-- Time to render name section of link id 24083: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees. We distribute the package under the BSD License. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).<\/p>\n<!-- Time to render link large description section of link id 24083: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Newick_Utilities> How to use <\/a>\n<!-- Time to render notes section of link id 24083: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24083: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/TravisWheelerLab\/NINJA\" id=\"link-24416\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NINJA<\/a>\n<!-- Time to render name section of link id 24416: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Nearly Infinite Neighbor Joining Application<\/p>\n<!-- Time to render link large description section of link id 24416: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NINJA> How to use <\/a>\n<!-- Time to render notes section of link id 24416: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24416: 0.00018477439880371 --> \n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/orthagogue\/\" id=\"link-23968\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">orthAgogue<\/a>\n<!-- Time to render name section of link id 23968: 2.8610229492188E-6 --> \n<\/td>\n<td><p>a tool for high speed estimation of homology relations within and between species in massive data sets. orthAgogue is easy to use and offers flexibility through a range of optional parameters.<\/p>\n<!-- Time to render link large description section of link id 23968: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23968: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23968: 0.00018596649169922 --> \n<tr><td><a href=\"https:\/\/github.com\/davidemms\/OrthoFinder\" id=\"link-23920\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OrthoFinder<\/a>\n<!-- Time to render name section of link id 23920: 3.814697265625E-6 --> \n<\/td>\n<td><p>OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.<\/p>\n<!-- Time to render link large description section of link id 23920: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OrthoFinder> How to use <\/a>\n<!-- Time to render notes section of link id 23920: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23920: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/MikkelSchubert\/paleomix\/wiki\/Overview\" id=\"link-23684\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PALEOMIX<\/a>\n<!-- Time to render name section of link id 23684: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The PALEOMIX pipeline is a set of free and open-source pipelines and tools designed to enable the rapid processing of Next Generation Sequencing (NGS) data, starting from de-multiplexed reads from one or more samples, through sequence processing and alignment, and ending with genotyping, phylogenetic inference on the samples, as well as metagenomic analysis of the samples.<\/p>\n<!-- Time to render link large description section of link id 23684: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PALEOMIX> How to use <\/a>\n<!-- Time to render notes section of link id 23684: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23684: 0.00017285346984863 --> \n<tr><td><a href=\"http:\/\/abacus.gene.ucl.ac.uk\/software\/paml.html\" id=\"link-23685\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PAML<\/a>\n<!-- Time to render name section of link id 23685: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.<\/p>\n<!-- Time to render link large description section of link id 23685: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PAML> How to use <\/a>\n<!-- Time to render notes section of link id 23685: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23685: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/pantools.readthedocs.io\/en\/latest\/\" id=\"link-25000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanTools<\/a>\n<!-- Time to render name section of link id 25000: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PanTools is a toolkit for comparative analysis of large number of genomes.<\/p>\n<!-- Time to render link large description section of link id 25000: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanTools> How to use <\/a>\n<!-- Time to render notes section of link id 25000: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25000: 0.00017118453979492 --> \n<tr><td><a href=\"https:\/\/github.com\/BenoitMorel\/ParGenes\" id=\"link-24432\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ParGenes<\/a>\n<!-- Time to render name section of link id 24432: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A massively parallel tool for model selection and tree inference on thousands of genes.<\/p>\n<!-- Time to render link large description section of link id 24432: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24432: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24432: 0.00017380714416504 --> \n<tr><td><a href=\"http:\/\/www.robertlanfear.com\/partitionfinder\/\" id=\"link-23686\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PartitionFinder<\/a>\n<!-- Time to render name section of link id 23686: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.<\/p>\n<!-- Time to render link large description section of link id 23686: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PartitionFinder> How to use <\/a>\n<!-- Time to render notes section of link id 23686: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23686: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/git-r3lab.uni.lu\/laura.denies\/PathoFact\" id=\"link-24434\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PathoFact<\/a>\n<!-- Time to render name section of link id 24434: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance.<\/p>\n<!-- Time to render link large description section of link id 24434: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24434: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24434: 0.00017404556274414 --> \n<tr><td><a href=\"https:\/\/github.com\/ruidlpm\/pathPhynder\" id=\"link-25161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pathPhynder<\/a>\n<!-- Time to render name section of link id 25161: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A workflow for integrating ancient lineages into present-day phylogenies.<\/p>\n<!-- Time to render link large description section of link id 25161: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pathPhynder> How to use <\/a>\n<!-- Time to render notes section of link id 25161: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25161: 0.00017094612121582 --> \n<tr><td><a href=\"http:\/\/phylosolutions.com\/paup-test\/\" id=\"link-23873\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PAUP<\/a>\n<!-- Time to render name section of link id 23873: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tools for inferring and interpreting phylogenetic trees<\/p>\n<!-- Time to render link large description section of link id 23873: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PAUP> How to use <\/a>\n<!-- Time to render notes section of link id 23873: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23873: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/gitlab.in2p3.fr\/phoogle\/pelican\" id=\"link-25083\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pelican<\/a>\n<!-- Time to render name section of link id 25083: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Pelican is a reimplementation of the model of Tamuri et al. (2009) to identify sites undergoing different kinds of directional selection in different parts of a phylogenetic tree.<\/p>\n<!-- Time to render link large description section of link id 25083: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pelican> How to use <\/a>\n<!-- Time to render notes section of link id 25083: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25083: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/www.bioinf.man.ac.uk\/resources\/phase\/\" id=\"link-23772\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHASE<\/a>\n<!-- Time to render name section of link id 23772: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PHASE is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.<\/p>\n<!-- Time to render link large description section of link id 23772: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHASE> How to use <\/a>\n<!-- Time to render notes section of link id 23772: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23772: 0.00017404556274414 --> \n<tr><td><a href=\"http:\/\/compgen.cshl.edu\/phast\/\" id=\"link-24866\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHAST<\/a>\n<!-- Time to render name section of link id 24866: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Phylogenetic Analysis with Space\/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics.<\/p>\n<!-- Time to render link large description section of link id 24866: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHAST> How to use <\/a>\n<!-- Time to render notes section of link id 24866: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24866: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/www.maths.otago.ac.nz\/~dbryant\/software\/phimanual.pdf\" id=\"link-23864\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhiPack<\/a>\n<!-- Time to render name section of link id 23864: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The Phi Test is a simple, rapid, and statistically efficient test for recombination.<\/p>\n<!-- Time to render link large description section of link id 23864: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23864: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23864: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/JLSteenwyk\/PhyKIT\" id=\"link-24443\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyKIT<\/a>\n<!-- Time to render name section of link id 24443: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.<\/p>\n<!-- Time to render link large description section of link id 24443: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyKIT> How to use <\/a>\n<!-- Time to render notes section of link id 24443: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24443: 9.8943710327148E-5 --> \n<tr><td><a href=\"http:\/\/evolution.genetics.washington.edu\/phylip.html\" id=\"link-23691\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PHYLIP<\/a>\n<!-- Time to render name section of link id 23691: 2.1457672119141E-6 --> \n<\/td>\n<td><div>PHYLIP (PHYLogeny Inference Package), is a package composed by 34 programs dedicated to phylogeny inference. Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.<\/div>\n<!-- Time to render link large description section of link id 23691: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PHYLIP> How to use <\/a>\n<!-- Time to render notes section of link id 23691: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23691: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/megasun.bch.umontreal.ca\/People\/lartillot\/www\/download.html\" id=\"link-23692\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyloBayes<\/a>\n<!-- Time to render name section of link id 23692: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction and molecular dating using protein and nucleic acid alignments.<\/p>\n<!-- Time to render link large description section of link id 23692: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyloBayes> How to use <\/a>\n<!-- Time to render notes section of link id 23692: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23692: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/megasun.bch.umontreal.ca\/People\/lartillot\/www\/downloadmpi.html\" id=\"link-23872\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Phylobayes_MPI<\/a>\n<!-- Time to render name section of link id 23872: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhyloBayes (Lartillot et al, 2009) is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. With MPI.<\/p>\n<!-- Time to render link large description section of link id 23872: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyloBayes_MPI> How to use <\/a>\n<!-- Time to render notes section of link id 23872: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23872: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/hrgv.github.io\/phyloFlash\" id=\"link-25094\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phyloFlash<\/a>\n<!-- Time to render name section of link id 25094: 2.1457672119141E-6 --> \n<\/td>\n<td><p>phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.<\/p>\n<!-- Time to render link large description section of link id 25094: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_phyloFlash> How to use <\/a>\n<!-- Time to render notes section of link id 25094: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25094: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/bioinfocs.rice.edu\/phylonet\" id=\"link-24444\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyloNet<\/a>\n<!-- Time to render name section of link id 24444: 2.1457672119141E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 24444: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyloNet> How to use <\/a>\n<!-- Time to render notes section of link id 24444: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24444: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/nsegata\/phylophlan\/wiki\/Home\" id=\"link-24062\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyloPhlAn<\/a>\n<!-- Time to render name section of link id 24062: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. The pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations.<\/p>\n<!-- Time to render link large description section of link id 24062: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24062: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24062: 0.00010085105895996 --> \n<tr><td><a href=\"https:\/\/phyluce.readthedocs.io\" id=\"link-24445\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phyluce<\/a>\n<!-- Time to render name section of link id 24445: 1.9073486328125E-6 --> \n<\/td>\n<td><p>phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.<\/p>\n<!-- Time to render link large description section of link id 24445: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_phyluce> How to use <\/a>\n<!-- Time to render notes section of link id 24445: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24445: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/stephaneguindon\/phyml\" id=\"link-23693\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PhyML<\/a>\n<!-- Time to render name section of link id 23693: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PhyML is a phylogeny software based on the maximum-likelihood principle.<\/p>\n<!-- Time to render link large description section of link id 23693: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PhyML> How to use <\/a>\n<!-- Time to render notes section of link id 23693: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23693: 0.00010085105895996 --> \n<tr><td><a href=\"https:\/\/github.com\/FePhyFoFum\/phyx\" id=\"link-23957\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">phyx<\/a>\n<!-- Time to render name section of link id 23957: 1.9073486328125E-6 --> \n<\/td>\n<td><p>phyx performs phylogenetics analyses on trees and sequences.<\/p>\n<!-- Time to render link large description section of link id 23957: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23957: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23957: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/picrust\/picrust2\" id=\"link-23695\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PICRUSt<\/a>\n<!-- Time to render name section of link id 23695: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PICRUSt (pronounced \uff93pie crust\uff94) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.<\/p>\n<!-- Time to render link large description section of link id 23695: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PICRUSt2> How to use <\/a>\n<!-- Time to render notes section of link id 23695: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23695: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/nekokoe\/Plasmer\" id=\"link-25217\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Plasmer<\/a>\n<!-- Time to render name section of link id 25217: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.<\/p>\n<!-- Time to render link large description section of link id 25217: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Plasmer> How to use <\/a>\n<!-- Time to render notes section of link id 25217: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25217: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/plass\" id=\"link-24703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Plass<\/a>\n<!-- Time to render name section of link id 24703: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.<\/p>\n<!-- Time to render link large description section of link id 24703: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24703: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24703: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/jaumlrc\/ProphET\" id=\"link-24463\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProphET<\/a>\n<!-- Time to render name section of link id 24463: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ProphET, Prophage Estimation Tool: a standalone prophage sequence prediction tool with self-updating reference database.<\/p>\n<!-- Time to render link large description section of link id 24463: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24463: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24463: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/paulklemm_PHD\/proteinortho\" id=\"link-25229\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Proteinortho<\/a>\n<!-- Time to render name section of link id 25229: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Proteinortho is a tool to detect orthologous genes within different species.<\/p>\n<!-- Time to render link large description section of link id 25229: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Proteinortho> How to use <\/a>\n<!-- Time to render notes section of link id 25229: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25229: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/bvalot\/pyMLST\" id=\"link-24470\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pyMLST<\/a>\n<!-- Time to render name section of link id 24470: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python Mlst Local Search Tool.<\/p>\n<!-- Time to render link large description section of link id 24470: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pyMLST> How to use <\/a>\n<!-- Time to render notes section of link id 24470: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24470: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/qiime2.org\/\" id=\"link-23703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">QIIME<\/a>\n<!-- Time to render name section of link id 23703: 2.8610229492188E-6 --> \n<\/td>\n<td><p>QIIME (pronounced \"chime\") stands for Quantitative Insights Into ttMicrobial Ecology. QIIME is an open source software package for ttcomparison and analysis of microbial communities, primarily based on tthigh-throughput amplicon sequencing data (such as SSU rRNA) generated tton a variety of platforms, but also supporting analysis of other types ttof data (such as shotgun metagenomic data). QIIME takes users from tttheir raw sequencing output through initial analyses such as OTU ttpicking, taxonomic assignment, and construction of phylogenetic trees ttfrom representative sequences of OTUs, and through downstream ttstatistical analysis, visualization, and production of ttpublication-quality graphics. QIIME has been applied to single studies ttbased on billions of sequences from thousands of samples. ttttt<\/p>\n<!-- Time to render link large description section of link id 23703: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_QIIME> How to use <\/a>\n<!-- Time to render notes section of link id 23703: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23703: 0.00012922286987305 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/r8s\/\" id=\"link-24477\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">r8s<\/a>\n<!-- Time to render name section of link id 24477: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This package implements several methods to infer divergence times on a molecular phylogeny, using penalized likelihood, maximum likelihood and nonparametric rate smoothing methods. It also implements miscellaneous tree and character evolution models and tests.<\/p>\n<!-- Time to render link large description section of link id 24477: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24477: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24477: 0.00013089179992676 --> \n<tr><td><a href=\"https:\/\/github.com\/alachins\/raisd\" id=\"link-24482\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAiSD<\/a>\n<!-- Time to render name section of link id 24482: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RAiSD (Raised Accuracy in Sweep Detection) is a stand-alone software implementation of the \u03bc statistic for selective sweep detection.<\/p>\n<!-- Time to render link large description section of link id 24482: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAiSD> How to use <\/a>\n<!-- Time to render notes section of link id 24482: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24482: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/stamatak\/standard-RAxML\" id=\"link-23708\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAxML<\/a>\n<!-- Time to render name section of link id 23708: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.<\/p>\n<!-- Time to render link large description section of link id 23708: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAxML> How to use <\/a>\n<!-- Time to render notes section of link id 23708: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23708: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/amkozlov\/raxml-ng\" id=\"link-24003\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAxML-NG<\/a>\n<!-- Time to render name section of link id 24003: 9.5367431640625E-7 --> \n<\/td>\n<td><p>RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.<\/p>\n<!-- Time to render link large description section of link id 24003: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAxML-NG> How to use <\/a>\n<!-- Time to render notes section of link id 24003: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24003: 9.5844268798828E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/noahares\/raxtax\" id=\"link-25810\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">raxtax<\/a>\n<!-- Time to render name section of link id 25810: 2.1457672119141E-6 --> \n<\/td>\n<td><p>raxtax is a fast and efficient k-mer-based non-Bayesian taxonomic classifier for barcoding DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 25810: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_raxtax> How to use <\/a>\n<!-- Time to render notes section of link id 25810: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25810: 9.7036361694336E-5 --> \n<tr><td><a href=\"http:\/\/denovoassembler.sourceforge.net\/download.html\" id=\"link-23709\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ray<\/a>\n<!-- Time to render name section of link id 23709: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Assemble genomes in parallel using the message-passing interface<\/p>\n<!-- Time to render link large description section of link id 23709: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23709: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23709: 9.1075897216797E-5 --> \n<tr><td><a href=\"http:\/\/sourceforge.net\/projects\/rdp-classifier\/\" id=\"link-23710\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDP Classifier<\/a>\n<!-- Time to render name section of link id 23710: 1.9073486328125E-6 --> \n<\/td>\n<td><div>The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.<\/div>\n<!-- Time to render link large description section of link id 23710: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23710: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23710: 9.1075897216797E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/rdpstaff\/RDPTools\" id=\"link-23712\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDPTools<\/a>\n<!-- Time to render name section of link id 23712: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Collection of commonly used RDP Tools for easy building<\/p>\n<!-- Time to render link large description section of link id 23712: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RDPTools> How to use <\/a>\n<!-- Time to render notes section of link id 23712: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23712: 0.0001518726348877 --> \n<tr><td><a href=\"https:\/\/github.com\/dimitris-karapliafis\/RdRpCATCH\" id=\"link-25763\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RdRpCATCH<\/a>\n<!-- Time to render name section of link id 25763: 1.9073486328125E-6 --> \n<\/td>\n<td>A community effort to create a shared resource for HMM-based RdRp discovery \n<!-- Time to render link large description section of link id 25763: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RdRpCATCH> How to use <\/a>\n<!-- Time to render notes section of link id 25763: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25763: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/DessimozLab\/read2tree\" id=\"link-24959\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">read2tree<\/a>\n<!-- Time to render name section of link id 24959: 1.9073486328125E-6 --> \n<\/td>\n<td><p>read2tree is a software tool that allows to obtain alignment matrices for tree inference.<\/p>\n<!-- Time to render link large description section of link id 24959: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_read2tree> How to use <\/a>\n<!-- Time to render notes section of link id 24959: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24959: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/khyox\/recentrifuge\" id=\"link-25784\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Recentrifuge<\/a>\n<!-- Time to render name section of link id 25784: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Robust comparative analysis and contamination removal for metagenomics<\/p>\n<!-- Time to render link large description section of link id 25784: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Recentrifuge> How to use <\/a>\n<!-- Time to render notes section of link id 25784: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25784: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/cpouchon\/REFMAKER\" id=\"link-25264\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REFMAKER<\/a>\n<!-- Time to render name section of link id 25264: 2.1457672119141E-6 --> \n<\/td>\n<td><p>REFMAKER is a command-line and user-friendly pipeline providing different tools to create nuclear references from genomic assemblies of shotgun libraries.<\/p>\n<!-- Time to render link large description section of link id 25264: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REFMAKER> How to use <\/a>\n<!-- Time to render notes section of link id 25264: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25264: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/kamimrcht\/REINDEER\" id=\"link-24488\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REINDEER<\/a>\n<!-- Time to render name section of link id 24488: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Efficient indexing of k-mer presence and abundance in sequencing datasets.<\/p>\n<!-- Time to render link large description section of link id 24488: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REINDEER> How to use <\/a>\n<!-- Time to render notes section of link id 24488: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24488: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/myersgroup.github.io\/relate\/index.html\" id=\"link-26167\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">relate<\/a>\n<!-- Time to render name section of link id 26167: 8.1062316894531E-6 --> \n<\/td>\n<td><p>Software to estimate genome-wide genealogies for thousands of samples<\/p>\n<!-- Time to render link large description section of link id 26167: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_relate> How to use <\/a>\n<!-- Time to render notes section of link id 26167: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26167: 0.00063085556030273 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/resfinder\" id=\"link-26087\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ResFinder<\/a>\n<!-- Time to render name section of link id 26087: 7.1525573730469E-6 --> \n<\/td>\n<td><p>ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.<\/p>\n<!-- Time to render link large description section of link id 26087: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ResFinder> How to use <\/a>\n<!-- Time to render notes section of link id 26087: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26087: 0.00034499168395996 --> \n<tr><td><a href=\"https:\/\/revbayes.github.io\/\" id=\"link-24018\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RevBayes<\/a>\n<!-- Time to render name section of link id 24018: 5.9604644775391E-6 --> \n<\/td>\n<td><p>RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. However, the environment is quite general and can be useful for many complex modeling tasks.<\/p>\n<!-- Time to render link large description section of link id 24018: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24018: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24018: 0.00038695335388184 --> \n<tr><td><a href=\"https:\/\/github.com\/slowkoni\/rfmix\" id=\"link-23770\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RFMIX<\/a>\n<!-- Time to render name section of link id 23770: 7.1525573730469E-6 --> \n<\/td>\n<td><p>A discriminative method for local ancestry inference<\/p>\n<!-- Time to render link large description section of link id 23770: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rfmix> How to use <\/a>\n<!-- Time to render notes section of link id 23770: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23770: 0.00033307075500488 --> \n<tr><td><a href=\"https:\/\/github.com\/aberer\/RogueNaRok\" id=\"link-24502\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RogueNaRok<\/a>\n<!-- Time to render name section of link id 24502: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A versatile and scalable algorithm for rogue taxon identification.<\/p>\n<!-- Time to render link large description section of link id 24502: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24502: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24502: 0.00032997131347656 --> \n<tr><td><a href=\"https:\/\/github.com\/computations\/root_digger\" id=\"link-24961\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RootDigger<\/a>\n<!-- Time to render name section of link id 24961: 8.1062316894531E-6 --> \n<\/td>\n<td><p>RootDigger is a program that will, when given a MSA and an unrooted tree with branch lengths place a root on the given tree. For the foreseeable future, RootDigger will only support DNA data, as the method RootDigger uses is ineffective when using AA data.<\/p>\n<!-- Time to render link large description section of link id 24961: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RootDigger> How to use <\/a>\n<!-- Time to render notes section of link id 24961: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24961: 0.00050497055053711 --> \n<tr><td><a href=\"https:\/\/github.com\/AdmiralenOla\/Scoary\" id=\"link-24512\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scoary<\/a>\n<!-- Time to render name section of link id 24512: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits.<\/p>\n<!-- Time to render link large description section of link id 24512: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Scoary> How to use <\/a>\n<!-- Time to render notes section of link id 24512: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24512: 0.00034284591674805 --> \n<tr><td><a href=\"http:\/\/tree.bio.ed.ac.uk\/software\/seqgen\/\" id=\"link-23814\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Seq-Gen<\/a>\n<!-- Time to render name section of link id 23814: 6.1988830566406E-6 --> \n<\/td>\n<td><p>Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.<\/p>\n<!-- Time to render link large description section of link id 23814: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23814: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23814: 0.00033998489379883 --> \n<tr><td><a href=\"https:\/\/www.appliedbioinformatics.com.au\/Edwards\/index.php\/SGSGeneLoss\" id=\"link-24516\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SGSGeneLoss<\/a>\n<!-- Time to render name section of link id 24516: 3.814697265625E-6 --> \n<\/td>\n<td><p>Gene presence\/absence variation discovery.<\/p>\n<!-- Time to render link large description section of link id 24516: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24516: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24516: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/phylo42\/sherpas\" id=\"link-25986\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SHERPAS<\/a>\n<!-- Time to render name section of link id 25986: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A new, alignment-free genome recombination detection tool exploiting the idea of phylo-kmers (originally developed in RAPPAS, Linard et al. 2019) to accelerate the process by several orders of magnitude while keeping comparable accuracy.<\/p>\n<!-- Time to render link large description section of link id 25986: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SHERPAS> How to use <\/a>\n<!-- Time to render notes section of link id 25986: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25986: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/gatb.inria.fr\/software\/simka\/\" id=\"link-24676\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Simka<\/a>\n<!-- Time to render name section of link id 24676: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.<\/p>\n<!-- Time to render link large description section of link id 24676: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Simka> How to use <\/a>\n<!-- Time to render notes section of link id 24676: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24676: 0.00015687942504883 --> \n<tr><td><a href=\"https:\/\/github.com\/wwood\/singlem\" id=\"link-24519\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">singlem<\/a>\n<!-- Time to render name section of link id 24519: 3.814697265625E-6 --> \n<\/td>\n<td><p>SingleM is a tool to find the abundances of discrete operational taxonomic units (OTUs) directly from shotgun metagenome data, without heavy reliance on reference sequence databases. It is able to differentiate closely related species even if those species are from lineages new to science.<\/p>\n<!-- Time to render link large description section of link id 24519: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24519: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24519: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/www.ebi.ac.uk\/research\/goldman\/software\/slr\/\" id=\"link-24090\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLR<\/a>\n<!-- Time to render name section of link id 24090: 2.8610229492188E-6 --> \n<\/td>\n<td><p>SLR is a program to detect sites in coding DNA that are unusually conserved and\/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree.<\/p>\n<!-- Time to render link large description section of link id 24090: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SLR> How to use <\/a>\n<!-- Time to render notes section of link id 24090: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24090: 0.00016093254089355 --> \n<tr><td><a href=\"http:\/\/chibba.pgml.uga.edu\/snphylo\" id=\"link-23795\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPhylo<\/a>\n<!-- Time to render name section of link id 23795: 3.0994415283203E-6 --> \n<\/td>\n<td><p>a pipeline to generate a phylogenetic tree from huge SNP data<\/p>\n<!-- Time to render link large description section of link id 23795: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNPhylo> How to use <\/a>\n<!-- Time to render notes section of link id 23795: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23795: 0.00015687942504883 --> \n<tr><td><a href=\"https:\/\/github.com\/FePhyFoFum\/sortadate\" id=\"link-23958\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SortaDate<\/a>\n<!-- Time to render name section of link id 23958: 3.814697265625E-6 --> \n<\/td>\n<td><p>Scripts that you can use at different stages to attempt to find more clock-like genes. Generally, you would use these for dating analyses with another package<\/p>\n<!-- Time to render link large description section of link id 23958: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23958: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23958: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/maplesond\/spectre\" id=\"link-24069\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SPECTRE<\/a>\n<!-- Time to render name section of link id 24069: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A collection of Phylogenetics tools for creating and manipulating networks and trees.<\/p>\n<!-- Time to render link large description section of link id 24069: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24069: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24069: 0.00015711784362793 --> \n<tr><td><a href=\"https:\/\/github.com\/jtamames\/SqueezeMeta\" id=\"link-25492\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SqueezeMeta<\/a>\n<!-- Time to render name section of link id 25492: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A fully automated metagenomics pipeline, from reads to bins.<\/p>\n<!-- Time to render link large description section of link id 25492: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SqueezeMeta> How to use <\/a>\n<!-- Time to render notes section of link id 25492: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25492: 0.00024890899658203 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/software\/ssu-align\/\" id=\"link-24542\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SSU-ALIGN<\/a>\n<!-- Time to render name section of link id 24542: 3.0994415283203E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 24542: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24542: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24542: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/sumatra\/wikis\/home\" id=\"link-23744\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sumatra<\/a>\n<!-- Time to render name section of link id 23744: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Sumatra was developed by the LECA and aims to compute a great deal of sequence similarities in a fast and exact way, based on the length of the Longest Common Subsequence (LCS) between two sequences. Sequence clustering based on similarities is also available through Sumaclust.<\/p>\n<!-- Time to render link large description section of link id 23744: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sumatra> How to use <\/a>\n<!-- Time to render notes section of link id 23744: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23744: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/metageni\/SUPER-FOCUS\" id=\"link-24546\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SUPER-FOCUS<\/a>\n<!-- Time to render name section of link id 24546: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A tool for agile functional analysis of metagenomic data.<\/p>\n<!-- Time to render link large description section of link id 24546: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24546: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24546: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/dportik\/SuperCRUNCH\" id=\"link-24547\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SuperCRUNCH<\/a>\n<!-- Time to render name section of link id 24547: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and\/or local sequence data.<\/p>\n<!-- Time to render link large description section of link id 24547: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24547: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24547: 0.00019192695617676 --> \n<tr><td><a href=\"https:\/\/github.com\/torognes\/swarm\" id=\"link-23881\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">swarm<\/a>\n<!-- Time to render name section of link id 23881: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A robust and fast clustering method for amplicon-based studies.<\/p>\n<!-- Time to render link large description section of link id 23881: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_swarm> How to use <\/a>\n<!-- Time to render notes section of link id 23881: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23881: 0.00016307830810547 --> \n<tr><td><a href=\"http:\/\/pop-gen.eu\/wordpress\/software\/sweed\" id=\"link-24553\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SweeD<\/a>\n<!-- Time to render name section of link id 24553: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A parallel and checkpointable tool that implements a composite likelihood ratio test for detecting selective sweeps. SweeD is based on the SweepFinder algorithm (Nielsen et al. 2005). SweeD can calculate the theoretical SFS of a given demographic model (stepwise changes or with an exponential growth phase + stepwise changes) by using the method by \u017divkovi\u0107 and Stephan (2011).<\/p>\n<!-- Time to render link large description section of link id 24553: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SweeD> How to use <\/a>\n<!-- Time to render notes section of link id 24553: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24553: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/bluenote-1577\/sylph\" id=\"link-25651\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sylph<\/a>\n<!-- Time to render name section of link id 25651: 3.0994415283203E-6 --> \n<\/td>\n<td><p>sylph is a program that performs ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples.<\/p>\n<!-- Time to render link large description section of link id 25651: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sylph> How to use <\/a>\n<!-- Time to render notes section of link id 25651: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25651: 0.00016880035400391 --> \n<tr><td><a href=\"https:\/\/github.com\/jonchang\/tact\" id=\"link-24556\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TACT<\/a>\n<!-- Time to render name section of link id 24556: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models<\/p>\n<!-- Time to render link large description section of link id 24556: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24556: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24556: 0.00015711784362793 --> \n<tr><td><a href=\"https:\/\/bioinf.shenwei.me\/taxonkit\/\" id=\"link-24648\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TaxonKit<\/a>\n<!-- Time to render name section of link id 24648: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A Practical and Efficient NCBI Taxonomy Toolkit<\/p>\n<!-- Time to render link large description section of link id 24648: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TaxonKit> How to use <\/a>\n<!-- Time to render notes section of link id 24648: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24648: 0.00016689300537109 --> \n<tr><td><a href=\"https:\/\/github.com\/danimfernandes\/tkgwv2\" id=\"link-24564\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TKGWV2<\/a>\n<!-- Time to render name section of link id 24564: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TKGWV2 is a pipeline to estimate biological relatedness (1st, 2nd, and unrelated degrees) between individuals specifically aimed at ultra-low coverage ancient DNA data obtained from whole genome sequencing.<\/p>\n<!-- Time to render link large description section of link id 24564: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TKGWV2> How to use <\/a>\n<!-- Time to render notes section of link id 24564: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24564: 0.0001671314239502 --> \n<tr><td><a href=\"https:\/\/github.com\/hillerlab\/TOGA\" id=\"link-25357\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TOGA<\/a>\n<!-- Time to render name section of link id 25357: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost.<\/p>\n<!-- Time to render link large description section of link id 25357: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TOGA> How to use <\/a>\n<!-- Time to render notes section of link id 25357: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25357: 0.00014090538024902 --> \n<tr><td><a href=\"http:\/\/www.topali.org\" id=\"link-24566\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TOPALI-v2<\/a>\n<!-- Time to render name section of link id 24566: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops.<\/p>\n<!-- Time to render link large description section of link id 24566: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24566: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24566: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/treesoft.sourceforge.net\/treebest.shtml\" id=\"link-23843\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeBeST<\/a>\n<!-- Time to render name section of link id 23843: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.<\/p>\n<!-- Time to render link large description section of link id 23843: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23843: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23843: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/blackrim\/treePL\" id=\"link-23885\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">treePL<\/a>\n<!-- Time to render name section of link id 23885: 2.1457672119141E-6 --> \n<\/td>\n<td><p>treePL is a phylogenetic penalized likelihood program.<\/p>\n<!-- Time to render link large description section of link id 23885: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23885: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23885: 0.00012803077697754 --> \n<tr><td><a href=\"https:\/\/github.com\/uym2\/TreeShrink\" id=\"link-24084\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeShrink<\/a>\n<!-- Time to render name section of link id 24084: 3.0994415283203E-6 --> \n<\/td>\n<td><p>TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees.<\/p>\n<!-- Time to render link large description section of link id 24084: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TreeShrink> How to use <\/a>\n<!-- Time to render notes section of link id 24084: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24084: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/neherlab\/treetime\" id=\"link-24748\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeTime<\/a>\n<!-- Time to render name section of link id 24748: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction.<\/p>\n<!-- Time to render link large description section of link id 24748: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24748: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24748: 0.00011992454528809 --> \n<tr><td><a href=\"http:\/\/trimal.cgenomics.org\/introduction\" id=\"link-23753\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">trimAl<\/a>\n<!-- Time to render name section of link id 23753: 1.9073486328125E-6 --> \n<\/td>\n<td><p>trimAl: a tool for automated alignment trimmin<\/p>\n<!-- Time to render link large description section of link id 23753: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_trimAl> How to use <\/a>\n<!-- Time to render notes section of link id 23753: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23753: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/simonhmartin\/twisst\" id=\"link-25333\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Twisst<\/a>\n<!-- Time to render name section of link id 25333: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Topology weighting by iterative sampling of sub-trees.<\/p>\n<!-- Time to render link large description section of link id 25333: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Twisst> How to use <\/a>\n<!-- Time to render notes section of link id 25333: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25333: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/Aveglia\/vAMPirus\" id=\"link-25599\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vAMPirus<\/a>\n<!-- Time to render name section of link id 25599: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.<\/p>\n<!-- Time to render link large description section of link id 25599: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vAMPirus> How to use <\/a>\n<!-- Time to render notes section of link id 25599: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25599: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/Matthijnssenslab\/ViPER\" id=\"link-25686\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViPER<\/a>\n<!-- Time to render name section of link id 25686: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bioinformatics pipeline used in the Laboratory of Viral Metagenomics (KU Leuven) to trim and assemble paired-end Illumina reads, and classify resulting contigs.<\/p>\n<!-- Time to render link large description section of link id 25686: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ViPER> How to use <\/a>\n<!-- Time to render notes section of link id 25686: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25686: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/EBI-Metagenomics\/emg-viral-pipeline\" id=\"link-25366\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VIRify<\/a>\n<!-- Time to render name section of link id 25366: 1.9073486328125E-6 --> \n<\/td>\n<td><p>VIRify is a pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies.<\/p>\n<!-- Time to render link large description section of link id 25366: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VIRify> How to use <\/a>\n<!-- Time to render notes section of link id 25366: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25366: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/DrKaiyangZheng\/VITAP\" id=\"link-25764\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VITAP<\/a>\n<!-- Time to render name section of link id 25764: 1.9073486328125E-6 --> \n<\/td>\n<td>The viral taxonomic assignment pipeline \n<!-- Time to render link large description section of link id 25764: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=Howse <\/a>\n<!-- Time to render notes section of link id 25764: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25764: 0.00012707710266113 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/sverre-phd-work\/voyager\/src\/master\/\" id=\"link-25922\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Voyager<\/a>\n<!-- Time to render name section of link id 25922: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Rapid and efficient mapping algorithm for long sequencing reads with insertion- and deletion errors. Mapping long reads in Sorted Motif Distance Space.<\/p>\n<!-- Time to render link large description section of link id 25922: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Voyager> How to use <\/a>\n<!-- Time to render notes section of link id 25922: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25922: 0.00011420249938965 --> \n<tr><td><a href=\"https:\/\/github.com\/SunPengChuan\/wgdi\" id=\"link-25319\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WGDI<\/a>\n<!-- Time to render name section of link id 25319: 1.9073486328125E-6 --> \n<\/td>\n<td>WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments.\n<!-- Time to render link large description section of link id 25319: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WGDI> How to use <\/a>\n<!-- Time to render notes section of link id 25319: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25319: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/LottePronk\/whokaryote\" id=\"link-24594\" class=\"track_this_link \" rel=\"noopener noreferrer\">whokaryote<\/a>\n<!-- Time to render name section of link id 24594: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Classification of metagenomic contigs as eukaryotic\/prokaryotic using biology-based features.<\/p>\n<!-- Time to render link large description section of link id 24594: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_whokaryote> How to use <\/a>\n<!-- Time to render notes section of link id 24594: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24594: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/uym2\/wLogDate\" id=\"link-24596\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wLogDate<\/a>\n<!-- Time to render name section of link id 24596: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Molecular Dating using logarithmic penalty function. wLogDate is a method for dating phylogenetic trees. Given a phylogeny and either sampling times for leaves or calibration points for internal nodes, wLogDate outputs a \"dated\" tree that conforms to the sampling times or calibration points. It can also work with no sampling time or calibration points where it would simply turn the tree into ultrametric, fixing its height to a given value. Its optimization criterion is to minimize the variance of the mutation rates in log scale (hence the term logDate).<\/p>\n<!-- Time to render link large description section of link id 24596: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24596: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24596: 0.00011086463928223 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1130\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => 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--><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Population genetics<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/bitbucket.org\/wegmannlab\/abctoolbox\/src\/master\/\" id=\"link-23836\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ABCtoolbox<\/a>\n<!-- Time to render name section of link id 23836: 2.8610229492188E-6 --> \n<\/td>\n<td><p>BCtoolbox is a general-purpose program to perform Approximate Bayesian Computation. ABCtoolbox can be used for ABC inference on almost any type of model, including models arising in physics, biology or engineering.<\/p>\n<!-- Time to render link large description section of link id 23836: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23836: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23836: 0.00011992454528809 --> \n<tr><td><a href=\"http:\/\/genetics.med.harvard.edu\/reich\/Reich_Lab\/Software.html\" id=\"link-23580\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ADMIXTOOLS<\/a>\n<!-- Time to render name section of link id 23580: 2.8610229492188E-6 --> \n<\/td>\n<td><p>ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.<\/p>\n<!-- Time to render link large description section of link id 23580: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ADMIXTOOLS> How to use <\/a>\n<!-- Time to render notes section of link id 23580: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23580: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/dalexander.github.io\/admixture\/\" id=\"link-23581\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Admixture<\/a>\n<!-- Time to render name section of link id 23581: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.<\/p>\n<!-- Time to render link large description section of link id 23581: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ADMIXTURE> How to use <\/a>\n<!-- Time to render notes section of link id 23581: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23581: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/groups.csail.mit.edu\/cb\/alder\/\" id=\"link-23582\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ALDER<\/a>\n<!-- Time to render name section of link id 23582: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture<\/p>\n<!-- Time to render link large description section of link id 23582: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23582: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23582: 0.00010776519775391 --> \n<tr><td><a href=\"https:\/\/alphagenes.roslin.ed.ac.uk\/wp\/software\/alphaimpute\/\" id=\"link-24012\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlphaImpute<\/a>\n<!-- Time to render name section of link id 24012: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AlphaImpute is a software package for imputing and phasing genotype data in diploid populations with pedigree information.<\/p>\n<!-- Time to render link large description section of link id 24012: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24012: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24012: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/russcd\/Ancestry_HMM\" id=\"link-25245\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ancestry HMM<\/a>\n<!-- Time to render name section of link id 25245: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence.<\/p>\n<!-- Time to render link large description section of link id 25245: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Ancestry_HMM> How to use <\/a>\n<!-- Time to render notes section of link id 25245: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25245: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/hringbauer\/ancIBD\" id=\"link-25115\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ancIBD<\/a>\n<!-- Time to render name section of link id 25115: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Identify IBD segments between pairs of individuals in ancient human DNA data.<\/p>\r\n<p>The software package\u00a0<code class=\"docutils literal notranslate\"><span class=\"pre\">ancIBD<\/span><\/code>\u00a0detects Identity-by-Descent (IBD) segments in typical human aDNA data, implementing an algorithm described\u00a0<a class=\"reference external\" href=\"https:\/\/doi.org\/10.1101\/2023.03.08.531671\">in this preprint<\/a>. The input data are imputed and phased genotype data. The default parameters of\u00a0<code class=\"docutils literal notranslate\"><span class=\"pre\">ancIBD<\/span><\/code>\u00a0are optimized for imputed data using the software\u00a0<a class=\"reference external\" href=\"https:\/\/odelaneau.github.io\/GLIMPSE\/glimpse1\/index.html\">GLIMPSE<\/a>\u00a0using the 1000 Genome haplotype reference panel.<\/p>\r\n<p>Software documentation <a href=\"https:\/\/ancibd.readthedocs.io\/en\/latest\/\">here<\/a>.<\/p>\n<!-- Time to render link large description section of link id 25115: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ancIBD> How to use <\/a>\n<!-- Time to render notes section of link id 25115: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25115: 0.00011777877807617 --> \n<tr><td><a href=\"http:\/\/www.popgen.dk\/angsd\/index.php\/Main_Page#Overview\" id=\"link-23586\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ANGSD<\/a>\n<!-- Time to render name section of link id 23586: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities.<\/p>\n<!-- Time to render link large description section of link id 23586: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ANGSD> How to use <\/a>\n<!-- Time to render notes section of link id 23586: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23586: 0.00013208389282227 --> \n<tr><td><a href=\"https:\/\/github.com\/CshlSiepelLab\/argweaver\/\" id=\"link-26136\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ARGweaver<\/a>\n<!-- Time to render name section of link id 26136: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The ARGweaver\/ARGweaver-D software package contains programs and libraries for sampling and manipulating ancestral recombination graphs (ARGs).<\/p>\n<!-- Time to render link large description section of link id 26136: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ARGweaver> How to use <\/a>\n<!-- Time to render notes section of link id 26136: 2.1457672119141E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26136: 0.00013208389282227 --> \n<tr><td><a href=\"https:\/\/github.com\/PalamaraLab\/ASMC\" id=\"link-24750\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ASMC<\/a>\n<!-- Time to render name section of link id 24750: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Ascertained Sequentially Markovian Coalescent (contains ASMC and an extension, FastSMC, together with python bindings for both)<\/p>\n<!-- Time to render link large description section of link id 24750: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ASMC> How to use <\/a>\n<!-- Time to render notes section of link id 24750: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24750: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/macroevolution\/bamm\" id=\"link-23913\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BAMM<\/a>\n<!-- Time to render name section of link id 23913: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program for multimodel inference on speciation and trait evolution.<\/p>\n<!-- Time to render link large description section of link id 23913: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23913: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23913: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/laneatmore\/BAMscorer\" id=\"link-24745\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BAMscorer<\/a>\n<!-- Time to render name section of link id 24745: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BAMscorer can be used to conduct genomic assignment tests from BAM files. Assignments can be done on genomic regions, inversions, and whole-genome datasets.<\/p>\n<!-- Time to render link large description section of link id 24745: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24745: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24745: 0.00011014938354492 --> \n<tr><td><a href=\"http:\/\/cmpg.unibe.ch\/software\/bayescan\/\" id=\"link-23592\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayeScan<\/a>\n<!-- Time to render name section of link id 23592: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Detecting natural selection from population-bases genetic data using differences in alleles frequencies between populations.<\/p>\n<!-- Time to render link large description section of link id 23592: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BayeScan> How to use <\/a>\n<!-- Time to render notes section of link id 23592: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23592: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/devillemereuil\/bayescenv\" id=\"link-23963\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayeScEnv<\/a>\n<!-- Time to render name section of link id 23963: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.<\/p>\n<!-- Time to render link large description section of link id 23963: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23963: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23963: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/www1.montpellier.inra.fr\/CBGP\/software\/baypass\/\" id=\"link-23773\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayPass<\/a>\n<!-- Time to render name section of link id 23773: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and\/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).<\/p>\n<!-- Time to render link large description section of link id 23773: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BayPass> How to use <\/a>\n<!-- Time to render notes section of link id 23773: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23773: 0.00011110305786133 --> \n<tr><td><a href=\"http:\/\/faculty.washington.edu\/browning\/beagle\/beagle.html\" id=\"link-23594\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle<\/a>\n<!-- Time to render name section of link id 23594: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.<\/p>\n<!-- Time to render link large description section of link id 23594: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Beagle> How to use <\/a>\n<!-- Time to render notes section of link id 23594: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23594: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/B-UMMI\/chewBBACA\" id=\"link-26081\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chewBBACA<\/a>\n<!-- Time to render name section of link id 26081: 2.1457672119141E-6 --> \n<\/td>\n<td><p><strong>chewBBACA<\/strong>\u00a0is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg\/wgMLST) schemas and results. The \"BBACA\" stands for \"BSR-Based Allele Calling Algorithm\". BSR stands for BLAST Score Ratio as proposed by\u00a0<a href=\"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-2\" rel=\"nofollow\">Rasko DA et al.<\/a>. The \"chew\" part adds extra coolness to the name and could be thought of as \"Comprehensive and Highly Efficient Workflow\".<\/p>\n<!-- Time to render link large description section of link id 26081: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chewBBACA> How to use <\/a>\n<!-- Time to render notes section of link id 26081: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26081: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/circuitscape.org\" id=\"link-25517\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Circuitscape<\/a>\n<!-- Time to render name section of link id 25517: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Circuitscape borrows algorithms from electronic circuit theory to predict patterns of movement, gene flow, and genetic differentiation among plant and animal populations in heterogeneous landscapes.<\/p>\n<!-- Time to render link large description section of link id 25517: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Circuitscape> How to use <\/a>\n<!-- Time to render notes section of link id 25517: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25517: 0.00012779235839844 --> \n<tr><td><a href=\"http:\/\/clumpak.tau.ac.il\/\" id=\"link-23854\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CLUMPAK<\/a>\n<!-- Time to render name section of link id 23854: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Clustering Markov Packager Across K - was developed in order to aid users analyse the results of STRUCTURE-like programs. The software offers a few alternative modes of action, please go to the Help section for detailed about these modes.<\/p>\n<!-- Time to render link large description section of link id 23854: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CLUMPAK> How to use <\/a>\n<!-- Time to render notes section of link id 23854: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23854: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/stevemussmann\/Comp-D\" id=\"link-24183\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Comp-D<\/a>\n<!-- Time to render name section of link id 24183: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A program for comprehensive computation of D-statistics and population summaries (serial version).<\/p>\n<!-- Time to render link large description section of link id 24183: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24183: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24183: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/esrud\/currentNe\" id=\"link-25189\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">currentNE<\/a>\n<!-- Time to render name section of link id 25189: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Estimation of current effective population using artificial neural networks.<\/p>\n<!-- Time to render link large description section of link id 25189: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_currentNe> How to use <\/a>\n<!-- Time to render notes section of link id 25189: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25189: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/esrud\/currentNe2\" id=\"link-26128\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">currentNe2<\/a>\n<!-- Time to render name section of link id 26128: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Estimation of current effective population using artificial neural networks.<\/p>\n<!-- Time to render link large description section of link id 26128: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_currentNe2> How to use <\/a>\n<!-- Time to render notes section of link id 26128: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26128: 0.00017619132995605 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/gutenkunstlab\/dadi\" id=\"link-23612\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dadi<\/a>\n<!-- Time to render name section of link id 23612: 2.8610229492188E-6 --> \n<\/td>\n<td><p>dadi implements a method for demographic inference from genetic data, based on a diffusion approximation to the allele frequency spectrum.<\/p>\n<!-- Time to render link large description section of link id 23612: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dadi> How to use <\/a>\n<!-- Time to render notes section of link id 23612: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23612: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/dfe-alpha-k-e-w\/\" id=\"link-24827\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DFE-alpha<\/a>\n<!-- Time to render name section of link id 24827: 2.1457672119141E-6 --> \n<\/td>\n<td><p>DFE-alpha was initially written to estimate the distribution of fitness effects (DFE) of new deleterious mutations using within-species nucleotide polymorphism data.<\/p>\n<!-- Time to render link large description section of link id 24827: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DFE-alpha> How to use <\/a>\n<!-- Time to render notes section of link id 24827: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24827: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenomics\/DILS\" id=\"link-25777\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DILS<\/a>\n<!-- Time to render name section of link id 25777: 1.9073486328125E-6 --> \n<\/td>\n<td><p>DILS is a statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework.<\/p>\n<!-- Time to render link large description section of link id 25777: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DILS> How to use <\/a>\n<!-- Time to render notes section of link id 25777: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25777: 0.0001828670501709 --> \n<tr><td><a href=\"http:\/\/www1.montpellier.inra.fr\/CBGP\/diyabc\/\" id=\"link-23859\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIYABC<\/a>\n<!-- Time to render name section of link id 23859: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers.<\/p>\n<!-- Time to render link large description section of link id 23859: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23859: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23859: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/millanek\/Dsuite\" id=\"link-24204\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Dsuite<\/a>\n<!-- Time to render name section of link id 24204: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations\/species<\/p>\n<!-- Time to render link large description section of link id 24204: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Dsuite> How to use <\/a>\n<!-- Time to render notes section of link id 24204: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24204: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/isaacovercast\/easySFS\" id=\"link-24207\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">easySFS<\/a>\n<!-- Time to render name section of link id 24207: 3.0994415283203E-6 --> \n<\/td>\n<td><p>easySFS is a tool for the effective selection of population size projection for construction of the site frequency spectrum. It may be used to convert VCF to dadi\/fastsimcoal\/momi2 style SFS for demographic analysis.<\/p>\n<!-- Time to render link large description section of link id 24207: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_easySFS> How to use <\/a>\n<!-- Time to render notes section of link id 24207: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24207: 0.00017714500427246 --> \n<tr><td><a href=\"https:\/\/github.com\/dipetkov\/eems\" id=\"link-23791\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EEMS<\/a>\n<!-- Time to render name section of link id 23791: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples.<\/p>\n<!-- Time to render link large description section of link id 23791: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EEMS> How to use <\/a>\n<!-- Time to render notes section of link id 23791: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23791: 0.00011515617370605 --> \n<tr><td><a href=\"http:\/\/www.hsph.harvard.edu\/alkes-price\/software\/\" id=\"link-23619\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Eigensoft<\/a>\n<!-- Time to render name section of link id 23619: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).<\/p>\n<!-- Time to render link large description section of link id 23619: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EIGENSOFT> How to use <\/a>\n<!-- Time to render notes section of link id 23619: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23619: 0.00011992454528809 --> \n<tr><td><a href=\"http:\/\/www.haplotype.org\/index.html\" id=\"link-23806\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ELAI<\/a>\n<!-- Time to render name section of link id 23806: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The software performs local ancestry inference for admixed individuals.<\/p>\n<!-- Time to render link large description section of link id 23806: 5.9604644775391E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ELAI> How to use <\/a>\n<!-- Time to render notes section of link id 23806: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23806: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/genome.sph.umich.edu\/wiki\/EMMAX\" id=\"link-25060\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMMAX<\/a>\n<!-- Time to render name section of link id 25060: 2.1457672119141E-6 --> \n<\/td>\n<td><p><b>EMMAX<\/b>\u00a0is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.<\/p>\n<!-- Time to render link large description section of link id 25060: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMMAX> How to use <\/a>\n<!-- Time to render notes section of link id 25060: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25060: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/est-usfs\/\" id=\"link-24826\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">est-sfs<\/a>\n<!-- Time to render name section of link id 24826: 1.9073486328125E-6 --> \n<\/td>\n<td><p>est-sfs implements a maximum likelihood method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities for DNA sequence data.<\/p>\n<!-- Time to render link large description section of link id 24826: 0 --> \n<\/td>\n<td><strong> Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24826: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24826: 0.00011682510375977 --> \n<tr><td><a href=\"http:\/\/www.pierroton.inra.fr\/genetics\/labo\/Software\/Famoz\/\" id=\"link-24224\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FaMoz<\/a>\n<!-- Time to render name section of link id 24224: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FaMoz, a software written in the C language and in TclTk, uses likelihood calculation and simulation to perform parentage studies with codominant, dominant, cytoplasmic markers or combinations of the different types.<\/p>\n<!-- Time to render link large description section of link id 24224: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24224: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24224: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/e-jorsboe\/fastNGSadmix\" id=\"link-24229\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastNGSadmix<\/a>\n<!-- Time to render name section of link id 24229: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Program for infering admixture proportions and doing PCA with a single NGS sample. Inferences based on reference panel.<\/p>\n<!-- Time to render link large description section of link id 24229: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24229: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24229: 0.0001370906829834 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/nicofmay\/fastsimbac\" id=\"link-24021\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastSimBac<\/a>\n<!-- Time to render name section of link id 24021: 2.8610229492188E-6 --> \n<\/td>\n<td><p>FastSimBac is a simulator of the coalescent process with bacterial recombination that simulates genealogies spatially across chromosomes as a Markov process.<\/p>\n<!-- Time to render link large description section of link id 24021: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24021: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24021: 0.00012302398681641 --> \n<tr><td><a href=\"http:\/\/cmpg.unibe.ch\/software\/fastsimcoal2\/\" id=\"link-23625\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastsimcoal2<\/a>\n<!-- Time to render name section of link id 23625: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast sequential Markov coalescent simulation of genomic data under complex evolutionary models<\/p>\n<!-- Time to render link large description section of link id 23625: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastsimcoal2> How to use <\/a>\n<!-- Time to render notes section of link id 23625: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23625: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/rajanil.github.io\/fastStructure\/\" id=\"link-23626\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastStructure<\/a>\n<!-- Time to render name section of link id 23626: 1.9073486328125E-6 --> \n<\/td>\n<td><p>fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.<\/p>\n<!-- Time to render link large description section of link id 23626: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastStructure> How to use <\/a>\n<!-- Time to render notes section of link id 23626: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23626: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/view\/fbat-web-page\" id=\"link-23967\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FBAT<\/a>\n<!-- Time to render name section of link id 23967: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FBAT is an acronym for Family-Based Association Tests in genetic analyses. Family-based association designs, as opposed to case-control study designs, are particularly attractive, since they test for linkage as well as association, avoid spurious associations caused by admixture of populations, and are convenient for investigators interested in refining linkage findings in family samples.<\/p>\n<!-- Time to render link large description section of link id 23967: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23967: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23967: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.paintmychromosomes.com\/\" id=\"link-23628\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fineSTRUCTURE<\/a>\n<!-- Time to render name section of link id 23628: 1.9073486328125E-6 --> \n<\/td>\n<td><p>fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23628: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fineSTRUCTURE> How to use <\/a>\n<!-- Time to render notes section of link id 23628: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23628: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/browning-lab\/flare\" id=\"link-25560\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">flare<\/a>\n<!-- Time to render name section of link id 25560: 1.9073486328125E-6 --> \n<\/td>\n<td>The flare program uses a set of reference haplotypes to infer the ancestry of each allele in a set of admixed study samples. The flare program is fast, accurate, and memory-efficient.\n<!-- Time to render link large description section of link id 25560: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_flare> How to use <\/a>\n<!-- Time to render notes section of link id 25560: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25560: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/gphocs-dev\/G-PhoCS\" id=\"link-25558\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">G-PhoCS<\/a>\n<!-- Time to render name section of link id 25558: 2.1457672119141E-6 --> \n<\/td>\n<td>G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.\n<!-- Time to render link large description section of link id 25558: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_G-PhoCS> How to use <\/a>\n<!-- Time to render notes section of link id 25558: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25558: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/regevs\/gamma_smc\" id=\"link-25135\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gamma-SMC<\/a>\n<!-- Time to render name section of link id 25135: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This is an alternative and an upgrade of the widely used PSMC method, which infers population size trajectories from VCF files.<\/p>\n<!-- Time to render link large description section of link id 25135: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Gamma-SMC> How to use <\/a>\n<!-- Time to render notes section of link id 25135: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25135: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/kimura.univ-montp2.fr\/~rousset\/Genepop.htm\" id=\"link-24246\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Genepop<\/a>\n<!-- Time to render name section of link id 24246: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Population genetics software that computes estimates of F-statistics.<\/p>\n<!-- Time to render link large description section of link id 24246: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24246: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24246: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/danny-wilson\/genomegaMap\" id=\"link-25340\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">genomegaMap<\/a>\n<!-- Time to render name section of link id 25340: 1.9073486328125E-6 --> \n<\/td>\n<td>Within-species genome-wide dN\/dS estimation from very many genomes.\n<!-- Time to render link large description section of link id 25340: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_genomegaMap> How to use <\/a>\n<!-- Time to render notes section of link id 25340: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25340: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/software.broadinstitute.org\/software\/genomestrip\/\" id=\"link-23817\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeSTRiP<\/a>\n<!-- Time to render name section of link id 23817: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.<\/p>\n<!-- Time to render link large description section of link id 23817: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23817: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23817: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/pkalbers\/geva\" id=\"link-24252\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEVA<\/a>\n<!-- Time to render name section of link id 24252: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Genealogical Estimation of Variant Age. We have developed a method for estimating the age of genetic variants; that is, the time of origin of an allele through mutation at a single locus. Our approach, which we refer to as the Genealogical Estimation of Variant Age (GEVA), is similar to existing methods that involve coalescent modeling to infer the time to the most recent common ancestor (TMRCA) between individual genomes <13, 23, 24>. However, these methods typically operate on a discretized timescale <13>, utilize only a fraction of the information available in larger sample data <25>, or employ approximations to overcome computational complexity <14, 15, 26>.<\/p>\n<!-- Time to render link large description section of link id 24252: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24252: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24252: 0.00012493133544922 --> \n<tr><td><a href=\"https:\/\/github.com\/DRL\/gIMble\" id=\"link-24102\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gIMble<\/a>\n<!-- Time to render name section of link id 24102: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A genome-wide IM blockwise likelihood estimation toolkit<\/p>\n<!-- Time to render link large description section of link id 24102: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24102: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24102: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/esrud\/GONE2\" id=\"link-26127\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GONE2<\/a>\n<!-- Time to render name section of link id 26127: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Demographic history from the observed spectrum of linkage disequilibrium.<\/p>\n<!-- Time to render link large description section of link id 26127: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GONE2> How to use <\/a>\n<!-- Time to render notes section of link id 26127: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26127: 0.00039887428283691 --> \n<tr><td><a href=\"https:\/\/github.com\/lczech\/grenedalf\" id=\"link-25863\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">grenedalf<\/a>\n<!-- Time to render name section of link id 25863: 5.0067901611328E-6 --> \n<\/td>\n<td><p>grenedalf is a collection of commands for working with pool sequencing population genetic data.<\/p>\n<!-- Time to render link large description section of link id 25863: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_grenedalf> How to use <\/a>\n<!-- Time to render notes section of link id 25863: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25863: 0.00032496452331543 --> \n<tr><td><a href=\"http:\/\/www.well.ox.ac.uk\/~cfreeman\/software\/gwas\/gtool.html\" id=\"link-23792\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gtools<\/a>\n<!-- Time to render name section of link id 23792: 5.9604644775391E-6 --> \n<\/td>\n<td><p>GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.<\/p>\n<!-- Time to render link large description section of link id 23792: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23792: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23792: 0.00029897689819336 --> \n<tr><td><a href=\"https:\/\/github.com\/vibansal\/HapCUT2\" id=\"link-23841\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HapCUT2<\/a>\n<!-- Time to render name section of link id 23841: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Software tools for haplotype assembly from sequence data<\/p>\n<!-- Time to render link large description section of link id 23841: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HapCUT2> How to use <\/a>\n<!-- Time to render notes section of link id 23841: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23841: 0.0002598762512207 --> \n<tr><td><a href=\"https:\/\/forge-dga.jouy.inra.fr\/projects\/hapflk\/\" id=\"link-23640\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hapflk<\/a>\n<!-- Time to render name section of link id 23640: 4.0531158447266E-6 --> \n<\/td>\n<td><p>hapflk is a software implementing the hapFLK <1> and FLK <2> tests for the detection of selection signatures based on multiple population genotyping data.<\/p>\n<!-- Time to render link large description section of link id 23640: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hapflk> How to use <\/a>\n<!-- Time to render notes section of link id 23640: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23640: 0.0003209114074707 --> \n<tr><td><a href=\"https:\/\/github.com\/seppinho\/haplogrep-cmd\" id=\"link-24271\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haplogrep<\/a>\n<!-- Time to render name section of link id 24271: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Haplogrep is a command-line tool for mtDNA haplogroup classification.<\/p>\n<!-- Time to render link large description section of link id 24271: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24271: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24271: 0.0002129077911377 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/dmarnetto\/haplostrips\/src\/master\/\" id=\"link-25020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haplostrips<\/a>\n<!-- Time to render name section of link id 25020: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Haplostrips produce plots that depict variants in a genomic window among different samples. Visualize similarities between haplotypes with respect to a reference haplotype through haplotype clustering and sorting, useful for revealing hidden population structure.<\/p>\n<!-- Time to render link large description section of link id 25020: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Haplostrips> How to use <\/a>\n<!-- Time to render notes section of link id 25020: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25020: 0.00024080276489258 --> \n<tr><td><a href=\"https:\/\/github.com\/gvbarroso\/iSMC\" id=\"link-24326\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iSMC<\/a>\n<!-- Time to render name section of link id 24326: 5.9604644775391E-6 --> \n<\/td>\n<td><p>This software extend the sequentially Markovian coalescent model to jointly infer the spatial variation in recombination rate (rho) from a single pair of unphased genomes.<\/p>\n<!-- Time to render link large description section of link id 24326: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24326: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24326: 0.00030899047851562 --> \n<tr><td><a href=\"http:\/\/ldhat.sourceforge.net\/instructions.shtml\" id=\"link-23655\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LDhat<\/a>\n<!-- Time to render name section of link id 23655: 4.0531158447266E-6 --> \n<\/td>\n<td><p>LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.<\/p>\n<!-- Time to render link large description section of link id 23655: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23655: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23655: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenmethods\/LDhelmet\" id=\"link-23656\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LDhelmet<\/a>\n<!-- Time to render name section of link id 23656: 5.0067901611328E-6 --> \n<\/td>\n<td><p>LDhelmet performs statistical inference for fine-scale variable recombination rate estimation.<\/p>\n<!-- Time to render link large description section of link id 23656: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LDhelmet> How to use <\/a>\n<!-- Time to render notes section of link id 23656: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23656: 0.00031185150146484 --> \n<tr><td><a href=\"https:\/\/github.com\/joepickrell\/malder\" id=\"link-23786\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MALDER<\/a>\n<!-- Time to render name section of link id 23786: 5.9604644775391E-6 --> \n<\/td>\n<td><p>This is a version of ALDER (http:\/\/groups.csail.mit.edu\/cb\/alder\/) that has been modified to allow multiple admixture events.<\/p>\n<!-- Time to render link large description section of link id 23786: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MALDER> How to use <\/a>\n<!-- Time to render notes section of link id 23786: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23786: 0.00022697448730469 --> \n<tr><td><a href=\"https:\/\/www.staff.ncl.ac.uk\/richard.howey\/mapthin\/\" id=\"link-24365\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MapThin<\/a>\n<!-- Time to render name section of link id 24365: 5.0067901611328E-6 --> \n<\/td>\n<td><p>Reduce the number of SNPs in a gene marker dense map computed by PLINK. First, by eliminating linked SNPs. Then, by applying different criteria.<\/p>\n<!-- Time to render link large description section of link id 24365: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24365: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24365: 0.00030183792114258 --> \n<tr><td><a href=\"http:\/\/darlinglab.org\/mauve\/mauve.html\" id=\"link-23662\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mauve<\/a>\n<!-- Time to render name section of link id 23662: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics.\u00a0 Aligning whole genomes is a fundamentally different problem than aligning short sequences.<\/p>\n<!-- Time to render link large description section of link id 23662: 1.1920928955078E-6 --> \n<\/td>\n<td>><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Mauve> How to use <\/a>\n<!-- Time to render notes section of link id 23662: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23662: 0.00019598007202148 --> \n<tr><td><a href=\"https:\/\/peterbeerli.com\/migrate-html5\/index.html\" id=\"link-25550\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Migrate<\/a>\n<!-- Time to render name section of link id 25550: 5.0067901611328E-6 --> \n<\/td>\n<td>Migrate estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture.\n<!-- Time to render link large description section of link id 25550: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Migrate> How to use <\/a>\n<!-- Time to render notes section of link id 25550: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25550: 0.00025105476379395 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/mlst\" id=\"link-24394\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MLST<\/a>\n<!-- Time to render name section of link id 24394: 1.6212463378906E-5 --> \n<\/td>\n<td><p>Multi-Locus sequence Typing. The method enables investigators to determine the ST based on WGS data.<\/p>\n<!-- Time to render link large description section of link id 24394: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24394: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24394: 0.00029897689819336 --> \n<tr><td><a href=\"http:\/\/home.uchicago.edu\/rhudson1\/source\/mksamples.html\" id=\"link-23673\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ms<\/a>\n<!-- Time to render name section of link id 23673: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A program for generating samples under neutral models.<\/p>\n<!-- Time to render link large description section of link id 23673: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ms> How to use <\/a>\n<!-- Time to render notes section of link id 23673: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23673: 0.00019001960754395 --> \n<tr><td><a href=\"http:\/\/msbayes.sourceforge.net\/\" id=\"link-23947\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msBayes<\/a>\n<!-- Time to render name section of link id 23947: 4.0531158447266E-6 --> \n<\/td>\n<td><p>msBayes allows complex and flexible comparative phylogeographic inference.<\/p>\n<!-- Time to render link large description section of link id 23947: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23947: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23947: 0.00028300285339355 --> \n<tr><td><a href=\"https:\/\/github.com\/stschiff\/msmc\" id=\"link-23674\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msmc<\/a>\n<!-- Time to render name section of link id 23674: 4.0531158447266E-6 --> \n<\/td>\n<td><p>This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences<\/p>\n<!-- Time to render link large description section of link id 23674: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msmc> How to use <\/a>\n<!-- Time to render notes section of link id 23674: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23674: 0.00019216537475586 --> \n<tr><td><a href=\"https:\/\/github.com\/stschiff\/msmc2\" id=\"link-23799\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msmc2<\/a>\n<!-- Time to render name section of link id 23799: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data<\/p>\n<!-- Time to render link large description section of link id 23799: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msmc2> How to use <\/a>\n<!-- Time to render notes section of link id 23799: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23799: 0.00014090538024902 --> \n<tr><td><a href=\"https:\/\/github.com\/tskit-dev\/msprime\" id=\"link-25085\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msprime<\/a>\n<!-- Time to render name section of link id 25085: 2.8610229492188E-6 --> \n<\/td>\n<td><p dir=\"auto\"><code>msprime<\/code>\u00a0is a population genetics simulator based on\u00a0<a href=\"https:\/\/tskit.dev\/\" rel=\"nofollow\">tskit<\/a>. Msprime can simulate random ancestral histories for a sample of individuals (consistent with a given demographic model) under a range of different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral history (which can be produced by msprime or other programs supporting\u00a0<a href=\"https:\/\/tskit.dev\/\" rel=\"nofollow\">tskit<\/a>) under a variety of genome sequence evolution models.<\/p>\r\n<p dir=\"auto\">Please see the\u00a0<a href=\"https:\/\/tskit.dev\/msprime\/docs\/latest\/\" rel=\"nofollow\">documentation<\/a>\u00a0for more details<\/p>\n<!-- Time to render link large description section of link id 25085: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_msprime> How to use <\/a>\n<!-- Time to render notes section of link id 25085: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25085: 0.00021100044250488 --> \n<tr><td><a href=\"https:\/\/github.com\/mhinsch\/msums\" id=\"link-24061\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">msums<\/a>\n<!-- Time to render name section of link id 24061: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A program for the efficient computation of a number of population genetics summary statistics. msums can read ms-format data on (nearly) arbitrary numbers of populations.<\/p>\n<!-- Time to render link large description section of link id 24061: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24061: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24061: 0.00013017654418945 --> \n<tr><td><a href=\"https:\/\/github.com\/AI-sandbox\/neural-admixture\" id=\"link-25021\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Neural-ADMIXTURE<\/a>\n<!-- Time to render name section of link id 25021: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Neural ADMIXTURE is an unsupervised global ancestry inference technique based on ADMIXTURE. By using neural networks, Neural ADMIXTURE offers high quality ancestry assignments with a running time which is much faster than ADMIXTURE's.<\/p>\n<!-- Time to render link large description section of link id 25021: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Neural-ADMIXTURE> How to use <\/a>\n<!-- Time to render notes section of link id 25021: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25021: 0.00014495849609375 --> \n<tr><td><a href=\"https:\/\/github.com\/fgvieira\/ngsLD\" id=\"link-24728\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsLD<\/a>\n<!-- Time to render name section of link id 24728: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account.<\/p>\n<!-- Time to render link large description section of link id 24728: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ngsLD> How to use <\/a>\n<!-- Time to render notes section of link id 24728: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24728: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/ANGSD\/NgsRelate\" id=\"link-23867\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsRelate<\/a>\n<!-- Time to render name section of link id 23867: 2.1457672119141E-6 --> \n<\/td>\n<td><p>NgsRelate can be used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.<\/p>\n<!-- Time to render link large description section of link id 23867: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NgsRelate> How to use <\/a>\n<!-- Time to render notes section of link id 23867: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23867: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/mfumagalli\/ngsTools\" id=\"link-23681\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ngsTools<\/a>\n<!-- Time to render name section of link id 23681: 2.1457672119141E-6 --> \n<\/td>\n<td><p><b>ngsTools<\/b> is a collection of programs for population genetics analyses from NGS data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data.<\/p>\n<!-- Time to render link large description section of link id 23681: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ngsTools> How to use <\/a>\n<!-- Time to render notes section of link id 23681: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23681: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/alachins\/omegaplus\" id=\"link-24425\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">omegaplus<\/a>\n<!-- Time to render name section of link id 24425: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A scalable tool for rapid detection of selective sweeps in whole-genome datasets.<\/p>\n<!-- Time to render link large description section of link id 24425: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OmegaPlus> How to use <\/a>\n<!-- Time to render notes section of link id 24425: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24425: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/pcadmix\/home\" id=\"link-23688\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PCAdmix<\/a>\n<!-- Time to render name section of link id 23688: 5.0067901611328E-6 --> \n<\/td>\n<td><p><span style=\"font-family: Helvetica\">PCAdmix is a method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes.\u00a0 The method considers data chromosome by chromosome.<\/span><\/p>\n<!-- Time to render link large description section of link id 23688: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23688: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23688: 0.00014519691467285 --> \n<tr><td><a href=\"http:\/\/www.cmpg.unibe.ch\/software\/PGDSpider\/\" id=\"link-23690\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PGDSpider<\/a>\n<!-- Time to render name section of link id 23690: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances)<\/p>\n<!-- Time to render link large description section of link id 23690: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PGDSpider> How to use <\/a>\n<!-- Time to render notes section of link id 23690: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23690: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/MEEIBioinformaticsCenter\/phy-mer\" id=\"link-24442\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Phy-Mer<\/a>\n<!-- Time to render name section of link id 24442: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A novel alignment-free and reference-independent mitochondrial haplogroup classifier.<\/p>\n<!-- Time to render link large description section of link id 24442: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24442: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24442: 0.00010395050048828 --> \n<tr><td><a href=\"https:\/\/pixy.readthedocs.io\/en\/latest\/about.html\" id=\"link-25559\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pixy<\/a>\n<!-- Time to render name section of link id 25559: 4.0531158447266E-6 --> \n<\/td>\n<td>pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (\u03c0) and between (dxy) populations from a VCF.\n<!-- Time to render link large description section of link id 25559: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pixy> How to use <\/a>\n<!-- Time to render notes section of link id 25559: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25559: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/github.com\/beiko-lab\/PMERGE\" id=\"link-23993\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PMERGE<\/a>\n<!-- Time to render name section of link id 23993: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PMERGE, is a software, which implements a new method that identifies candidate PSVs by building networks of loci that share high levels of nucleotide similarity. The PMERGE is embedded in the analysis pipeline of the widely used Stacks software, and it is straightforward to apply it as an additional filter in population-genomic studies using RAD-seq data.<\/p>\n<!-- Time to render link large description section of link id 23993: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23993: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23993: 0.00015997886657715 --> \n<tr><td><a href=\"http:\/\/brown.edu\/Research\/Ramachandran_Lab\/projects\/\" id=\"link-23983\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pong<\/a>\n<!-- Time to render name section of link id 23983: 3.0994415283203E-6 --> \n<\/td>\n<td><p>pong is a freely available software package, released by Behr et al. (2016, Bioinformatics), for post-processing output from clustering inference using population genetic data.<\/p>\n<!-- Time to render link large description section of link id 23983: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23983: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23983: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/popart.maths.otago.ac.nz\/\" id=\"link-25731\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PopART<\/a>\n<!-- Time to render name section of link id 25731: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PopART (Population Analysis with Reticulate Trees) is free, open source population genetics software that was developed as part of the Allan Wilson Centre Imaging Evolution Initiative.<\/p>\n<!-- Time to render link large description section of link id 25731: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PopART> How to use <\/a>\n<!-- Time to render notes section of link id 25731: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25731: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/bkehr\/popins\" id=\"link-23849\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">popins<\/a>\n<!-- Time to render name section of link id 23849: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Population-scale detection of novel-sequence insertions.<\/p>\n<!-- Time to render link large description section of link id 23849: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23849: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23849: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/popoolation\/?source=navbar\" id=\"link-25272\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PoPoolation<\/a>\n<!-- Time to render name section of link id 25272: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima\u2019s Pi, Watterson\u2019s Theta and Tajima\u2019s D with a sliding window approach for chromosomes or for set of genes.<\/p>\n<!-- Time to render link large description section of link id 25272: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PoPoolation> How to use <\/a>\n<!-- Time to render notes section of link id 25272: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25272: 0.00016617774963379 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/popoolation2\/\" id=\"link-23930\" class=\"track_this_link \" rel=\"noopener noreferrer\">PoPoolation2<\/a>\n<!-- Time to render name section of link id 23930: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution.<\/p>\n<!-- Time to render link large description section of link id 23930: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PoPoolation2> How to use <\/a>\n<!-- Time to render notes section of link id 23930: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23930: 0.0001218318939209 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenomics\/popPhylABC\" id=\"link-24459\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">popPhylABC<\/a>\n<!-- Time to render name section of link id 24459: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Scripts used for ABC analysis with homo- and heterogeneity in Migration rates or\/and Effective population sizes<\/p>\n<!-- Time to render link large description section of link id 24459: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24459: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24459: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/psmc\" id=\"link-23856\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">psmc<\/a>\n<!-- Time to render name section of link id 23856: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This software package infers population size history from a diploid sequence<br \/>\r\nusing the Pairwise Sequentially Markovian Coalescent (PSMC) model.<\/p>\n<!-- Time to render link large description section of link id 23856: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_psmc> How to use <\/a>\n<!-- Time to render notes section of link id 23856: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23856: 0.00014901161193848 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenmethods\/pyrho\" id=\"link-25294\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pyrho<\/a>\n<!-- Time to render name section of link id 25294: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Fast demography-aware inference of fine-scale recombination rates based on fused-LASSO.<\/p>\n<!-- Time to render link large description section of link id 25294: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pyrho> How to use <\/a>\n<!-- Time to render notes section of link id 25294: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25294: 0.00015592575073242 --> \n<tr><td><a href=\"https:\/\/github.com\/TCLamnidis\/qpWrapper\" id=\"link-24474\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">qpWrapper<\/a>\n<!-- Time to render name section of link id 24474: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tools allowing to launch qpAdmn analyzes (Admixtools) in series on a list of individuals.<\/p>\n<!-- Time to render link large description section of link id 24474: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24474: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24474: 0.0001368522644043 --> \n<tr><td><a href=\"https:\/\/github.com\/pephco\/quickLD\" id=\"link-25289\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quickLD<\/a>\n<!-- Time to render name section of link id 25289: 2.8610229492188E-6 --> \n<\/td>\n<td><p>High-performance Computation of Linkage Disequilibrium on CPUs and GPUs.<\/p>\n<!-- Time to render link large description section of link id 25289: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_quickLD> How to use <\/a>\n<!-- Time to render notes section of link id 25289: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25289: 0.0001518726348877 --> \n<tr><td><a href=\"https:\/\/myersgroup.github.io\/relate\/index.html\" id=\"link-26167\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">relate<\/a>\n<!-- Time to render name section of link id 26167: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software to estimate genome-wide genealogies for thousands of samples<\/p>\n<!-- Time to render link large description section of link id 26167: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_relate> How to use <\/a>\n<!-- Time to render notes section of link id 26167: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26167: 0.00017094612121582 --> \n<tr><td><a href=\"https:\/\/github.com\/slowkoni\/rfmix\" id=\"link-23770\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RFMIX<\/a>\n<!-- Time to render name section of link id 23770: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A discriminative method for local ancestry inference<\/p>\n<!-- Time to render link large description section of link id 23770: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rfmix> How to use <\/a>\n<!-- Time to render notes section of link id 23770: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23770: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/sccmecfinder\" id=\"link-24511\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SCCmecFinder<\/a>\n<!-- Time to render name section of link id 24511: 2.8610229492188E-6 --> \n<\/td>\n<td><p>SCCmecFinder identifies SCCmec elements in sequenced S. aureus isolates.<\/p>\n<!-- Time to render link large description section of link id 24511: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SCCmecFinder> How to use <\/a>\n<!-- Time to render notes section of link id 24511: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24511: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/scrm.github.io\/\" id=\"link-23883\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">scrm<\/a>\n<!-- Time to render name section of link id 23883: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A coalescent simulator for genome-scale sequences.<\/p>\n<!-- Time to render link large description section of link id 23883: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23883: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23883: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/github.com\/szpiech\/selscan\" id=\"link-23725\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">selscan<\/a>\n<!-- Time to render name section of link id 23725: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program to calculate EHH-based scans for positive selection in genomes.<\/p>\n<!-- Time to render link large description section of link id 23725: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_selscan> How to use <\/a>\n<!-- Time to render notes section of link id 23725: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23725: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/phylo42\/sherpas\" id=\"link-25986\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SHERPAS<\/a>\n<!-- Time to render name section of link id 25986: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A new, alignment-free genome recombination detection tool exploiting the idea of phylo-kmers (originally developed in RAPPAS, Linard et al. 2019) to accelerate the process by several orders of magnitude while keeping comparable accuracy.<\/p>\n<!-- Time to render link large description section of link id 25986: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SHERPAS> How to use <\/a>\n<!-- Time to render notes section of link id 25986: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25986: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/simupop.sourceforge.net\/Main\/HomePage\" id=\"link-23730\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">simuPOP<\/a>\n<!-- Time to render name section of link id 23730: 2.1457672119141E-6 --> \n<\/td>\n<td><p>simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.<\/p>\n<!-- Time to render link large description section of link id 23730: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23730: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23730: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/messerlab.org\/slim\/\" id=\"link-23831\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLiM<\/a>\n<!-- Time to render name section of link id 23831: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.<\/p>\n<!-- Time to render link large description section of link id 23831: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SLiM> How to use <\/a>\n<!-- Time to render notes section of link id 23831: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23831: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/popgenmethods\/smcpp\" id=\"link-24522\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SMC++<\/a>\n<!-- Time to render name section of link id 24522: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SMC++ is a program for estimating the size history of populations from whole genome sequence data.<\/p>\n<!-- Time to render link large description section of link id 24522: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SMC++> How to use <\/a>\n<!-- Time to render notes section of link id 24522: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24522: 9.8943710327148E-5 --> \n<tr><td><a href=\"http:\/\/membres-timc.imag.fr\/Olivier.Francois\/snmf\/index.htm\" id=\"link-23998\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sNMF<\/a>\n<!-- Time to render name section of link id 23998: 1.1920928955078E-6 --> \n<\/td>\n<td><p>A fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics.<\/p>\n<!-- Time to render link large description section of link id 23998: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23998: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23998: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/HCGB-IGTP\/spaTyper\" id=\"link-24532\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spaTyper<\/a>\n<!-- Time to render name section of link id 24532: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Computational method for finding spa types. Staphylococcus aureus\u00a0is a major human pathogen causing skin and tissue infections, pneumonia, septicemia, and device-associated infections. The emergence of strains resistant to methicillin (MRSA) and other antibacterial agents has become a major concern, especially in the hospital environment, because of the high mortality of the infections caused by these strains. Single locus DNA-sequencing of the repeat region of the\u00a0Staphylococcus\u00a0protein A gene (spa) can be used for reliable, accurate and discriminatory typing of MRSA. Repeats are assigned a numerical code and the spa-type is deduced from the order of specific repeats. However, spa-typing was hampered in the past by the lack of a consensus on assignments of new spa-repeats and -types.<\/p>\n<!-- Time to render link large description section of link id 24532: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24532: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24532: 0.00010108947753906 --> \n<tr><td><a href=\"https:\/\/sites.google.com\/site\/jpopgen\/stairway-plot\" id=\"link-24032\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">stairway_plot<\/a>\n<!-- Time to render name section of link id 24032: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data. It does not need a pre-defined population model and can be applied to hundreds of unphased sequences.<\/p>\n<!-- Time to render link large description section of link id 24032: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_stairway_plot> How to use <\/a>\n<!-- Time to render notes section of link id 24032: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24032: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/web.stanford.edu\/group\/pritchardlab\/home.html\" id=\"link-23742\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Structure<\/a>\n<!-- Time to render name section of link id 23742: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The program <b>structure<\/b> is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.<\/p>\n<!-- Time to render link large description section of link id 23742: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Structure> How to use <\/a>\n<!-- Time to render notes section of link id 23742: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23742: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/mourisl\/T1K\" id=\"link-26025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T1K<\/a>\n<!-- Time to render name section of link id 26025: 1.9073486328125E-6 --> \n<\/td>\n<td><p>T1K (The ONE genotyper for Kir and HLA) is a computational tool to infer the alleles for the polymorphic genes such as KIR and HLA. T1K calculates the allele abundances based on the RNA-seq\/WES\/WGS read alignments on the provided allele reference sequences. The abundances are used to pick the true alleles for each gene. T1K provides the post analysis steps, including novel SNP detection and single-cell representation. T1K supports both single-end and paired-end sequencing data with any read length.<\/p>\n<!-- Time to render link large description section of link id 26025: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_T1K> How to use <\/a>\n<!-- Time to render notes section of link id 26025: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26025: 0.00010085105895996 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/treemix\/\" id=\"link-23751\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TreeMix<\/a>\n<!-- Time to render name section of link id 23751: 1.9073486328125E-6 --> \n<\/td>\n<td><p><i>TreeMix<\/i> is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.<\/p>\n<!-- Time to render link large description section of link id 23751: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TreeMix> How to use <\/a>\n<!-- Time to render notes section of link id 23751: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23751: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/bacpop\/unitig-caller\" id=\"link-25656\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">unitig-caller<\/a>\n<!-- Time to render name section of link id 25656: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Methods to determine sequence element (unitig) presence\/absence.<\/p>\n<!-- Time to render link large description section of link id 25656: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_unitig-caller> How to use <\/a>\n<!-- Time to render notes section of link id 25656: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25656: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/bmvdgeijn\/WASP\" id=\"link-25991\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WASP<\/a>\n<!-- Time to render name section of link id 25991: 2.1457672119141E-6 --> \n<\/td>\n<td><p>WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs.<\/p>\n<!-- Time to render link large description section of link id 25991: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WASP> How to use <\/a>\n<!-- Time to render notes section of link id 25991: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25991: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/genid\/Yleaf\" id=\"link-24599\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Yleaf<\/a>\n<!-- Time to render name section of link id 24599: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software for human Y-chromosomal haplogroup inference from next generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24599: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Yleaf> How to use <\/a>\n<!-- Time to render notes section of link id 24599: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24599: 0.00010800361633301 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1143\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [field] => term_id\n                            [terms] => 1143\n                            [include_children] => \n                        )\n\n                )\n\n            [post_status] => Array\n                (\n                    [0] => publish\n                )\n\n            [orderby] => Array\n                (\n                    [title] => ASC\n                )\n\n        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Array\n                (\n                    [0] => wp_term_relationships\n                )\n\n            [queried_terms] => Array\n                (\n                    [link_library_category] => Array\n                        (\n                            [terms] => Array\n                                (\n                                    [0] => 1143\n                                )\n\n                            [field] => term_id\n                        )\n\n                )\n\n            [primary_table] => wp_posts\n            [primary_id_column] => ID\n        )\n\n    [meta_query] => WP_Meta_Query Object\n        (\n            [queries] => Array\n                (\n                )\n\n            [relation] => \n            [meta_table] => \n            [meta_id_column] => \n            [primary_table] => \n            [primary_id_column] => \n            [table_aliases:protected] => Array\n                (\n                )\n\n            [clauses:protected] => Array\n                (\n                )\n\n            [has_or_relation:protected] => \n        )\n\n    [date_query] => \n    [request] => \n\t\t\tSELECT   wp_posts.*\n\t\t\tFROM wp_posts  LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1143)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 24060\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:49\n                    [post_date_gmt] => 2022-11-22 09:25:49\n                    [post_content] => \n                    [post_title] => CRISPOR\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => crispor\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:14:48\n                    [post_modified_gmt] => 2025-05-21 06:14:48\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/crispor\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 24347\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:10\n                    [post_date_gmt] => 2022-11-22 09:26:10\n                    [post_content] => \n                    [post_title] => lima\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => lima\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:15:05\n                    [post_modified_gmt] => 2025-05-22 07:15:05\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/lima\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n          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2024-09-20 17:21:15\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25501\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n        )\n\n    [post_count] => 4\n    [current_post] => -1\n    [in_the_loop] => \n    [post] => WP_Post Object\n        (\n            [ID] => 24060\n            [post_author] => 5\n            [post_date] => 2022-11-22 10:25:49\n            [post_date_gmt] => 2022-11-22 09:25:49\n            [post_content] => \n            [post_title] => CRISPOR\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => crispor\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2025-05-21 08:14:48\n            [post_modified_gmt] => 2025-05-21 06:14:48\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/crispor\/\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 4\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    [is_category] => \n    [is_tag] => \n    [is_tax] => 1\n    [is_search] => \n    [is_feed] => \n    [is_comment_feed] => \n    [is_trackback] => \n    [is_home] => \n    [is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => 626064615eb9bb77027bd748199ea199\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.00093698501586914-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1143 level0\"><!-- Div Category --><div id=\"primers\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Primers<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/maximilianh\/crisporWebsite\" id=\"link-24060\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRISPOR<\/a>\n<!-- Time to render name section of link id 24060: 3.0994415283203E-6 --> \n<\/td>\n<td><p>CRISPOR predicts off-targets in the genome, ranks guides, highlights problematic guides, designs primers and helps with cloning.<\/p>\n<!-- Time to render link large description section of link id 24060: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CRISPOR> How to use <\/a>\n<!-- Time to render notes section of link id 24060: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24060: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/pacificbiosciences\/barcoding\/\" id=\"link-24347\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lima<\/a>\n<!-- Time to render name section of link id 24347: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Demultiplex Barcoded PacBio Samples.<\/p>\n<!-- Time to render link large description section of link id 24347: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24347: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24347: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/calacademy-research\/minibar\" id=\"link-25619\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">minibar<\/a>\n<!-- Time to render name section of link id 25619: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Dual barcode and primer demultiplexing for MinION sequenced reads.<\/p>\n<!-- Time to render link large description section of link id 25619: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_minibar> How to use <\/a>\n<!-- Time to render notes section of link id 25619: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25619: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/shendurelab\/MIPGEN\" id=\"link-25501\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MIPgen<\/a>\n<!-- Time to render name section of link id 25501: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Use MIPgen to design custom mip panels for target enrichment of moderate to high complexity DNA targets ranging from 120 to 250bp in size.<\/p>\n<!-- Time to render link large description section of link id 25501: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MIPgen> How to use <\/a>\n<!-- Time to render notes section of link id 25501: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25501: 0.00010991096496582 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1119\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            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[post_name] => alphafold\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2023-07-08 11:56:56\n                    [post_modified_gmt] => 2023-07-08 09:56:56\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24913\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 25668\n                    [post_author] => 5\n                    [post_date] => 2025-02-12 07:53:22\n                    [post_date_gmt] => 2025-02-12 06:53:22\n                    [post_content] => \n                    [post_title] => AlphaFold-disorder\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alphafold-disorder\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-03-02 20:06:47\n                    [post_modified_gmt] => 2025-03-02 19:06:47\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25668\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 24137\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:05\n                    [post_date_gmt] => 2022-11-22 09:26:05\n                    [post_content] => \n                    [post_title] => Alphafold2-Pytorch\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alphafold2-pytorch\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:23:21\n                    [post_modified_gmt] => 2025-05-21 05:23:21\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/alphafold2-pytorch\/\n                    [menu_order] => 0\n                    [post_type] => 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\n                    [pinged] => \n                    [post_modified] => 2024-03-12 10:17:53\n                    [post_modified_gmt] => 2024-03-12 09:17:53\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25271\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [5] => WP_Post Object\n                (\n                    [ID] => 24180\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:08\n                    [post_date_gmt] => 2022-11-22 09:26:08\n                    [post_content] => \n                    [post_title] => CITE-seq-Count\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => cite-seq-count\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:10:15\n                    [post_modified_gmt] => 2025-05-21 06:10:15\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/cite-seq-count\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [6] => WP_Post Object\n                (\n                    [ID] => 24900\n                    [post_author] => 5\n                    [post_date] => 2023-06-20 14:55:27\n                    [post_date_gmt] => 2023-06-20 12:55:27\n                    [post_content] => \n                    [post_title] => ColabFold\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => colabfold\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2023-07-06 22:52:46\n                    [post_modified_gmt] => 2023-07-06 20:52:46\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24900\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n  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https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26224\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [8] => WP_Post Object\n                (\n                    [ID] => 23798\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:38\n                    [post_date_gmt] => 2022-11-22 09:25:38\n                    [post_content] => \n                    [post_title] => DIAMOND\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => diamond\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 13:57:36\n                    [post_modified_gmt] => 2025-05-21 11:57:36\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/diamond\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [9] => WP_Post Object\n                (\n                    [ID] => 26162\n                    [post_author] => 5\n                    [post_date] => 2025-12-08 09:52:33\n                    [post_date_gmt] => 2025-12-08 08:52:33\n                    [post_content] => \n                    [post_title] => DiffDock\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => diffdock\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-12-17 13:54:21\n                    [post_modified_gmt] => 2025-12-17 12:54:21\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26162\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [10] => WP_Post Object\n                (\n                    [ID] => 26173\n                    [post_author] => 5\n                    [post_date] => 2025-12-17 08:59:10\n                    [post_date_gmt] => 2025-12-17 07:59:10\n                    [post_content] => \n                    [post_title] => DTVF\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => dtvf\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-01-03 11:28:55\n                    [post_modified_gmt] => 2026-01-03 10:28:55\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26173\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 25295\n                    [post_author] => 5\n                    [post_date] => 2024-03-12 06:29:48\n                    [post_date_gmt] => 2024-03-12 05:29:48\n                    [post_content] => \n                    [post_title] => E2P2\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => e2p2\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-12 10:19:19\n                    [post_modified_gmt] => 2024-03-12 09:19:19\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25295\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [12] => WP_Post Object\n                (\n                    [ID] => 25748\n                    [post_author] => 5\n                    [post_date] => 2025-03-31 08:41:48\n                    [post_date_gmt] => 2025-03-31 06:41:48\n                    [post_content] => \n                    [post_title] => EGAPx\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => egapx\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-18 10:32:30\n                    [post_modified_gmt] => 2025-05-18 08:32:30\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25748\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [13] => WP_Post Object\n                (\n                    [ID] => 24920\n                    [post_author] => 5\n                    [post_date] => 2023-06-28 07:22:24\n                    [post_date_gmt] => 2023-06-28 05:22:24\n                    [post_content] => \n                    [post_title] => EMBER3D\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => ember3d\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2023-07-06 23:03:05\n                    [post_modified_gmt] => 2023-07-06 21:03:05\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24920\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [14] => WP_Post Object\n                (\n                    [ID] => 25330\n                    [post_author] => 5\n                    [post_date] => 2024-03-28 06:08:54\n                    [post_date_gmt] => 2024-03-28 05:08:54\n                    [post_content] => \n                    [post_title] => EVE\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => eve\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-28 14:05:23\n                    [post_modified_gmt] => 2024-03-28 13:05:23\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25330\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [15] => WP_Post Object\n                (\n                    [ID] => 25625\n                    [post_author] => 5\n                    [post_date] => 2025-01-08 06:32:21\n                    [post_date_gmt] => 2025-01-08 05:32:21\n                    [post_content] => \n                    [post_title] => EvoBind\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => evobind\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-03-02 20:13:04\n                    [post_modified_gmt] => 2025-03-02 19:13:04\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25625\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [16] => WP_Post Object\n                (\n                    [ID] => 25340\n                    [post_author] => 5\n                    [post_date] => 2024-04-04 07:22:02\n                    [post_date_gmt] => 2024-04-04 05:22:02\n                    [post_content] => \n                    [post_title] => genomegaMap\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => genomegamap\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-03 09:27:16\n                    [post_modified_gmt] => 2024-06-03 07:27:16\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => 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[post_modified] => 2025-03-12 09:55:10\n                    [post_modified_gmt] => 2025-03-12 08:55:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25667\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [18] => WP_Post Object\n                (\n                    [ID] => 23649\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 12:19:18\n                    [post_date_gmt] => 2022-11-22 11:19:18\n                    [post_content] => \n                    [post_title] => InterProScan\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => interproscan\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 07:37:10\n                    [post_modified_gmt] => 2025-05-22 05:37:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/interproscan\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [19] => WP_Post Object\n                (\n                    [ID] => 25471\n                    [post_author] => 5\n                    [post_date] => 2024-07-04 06:20:49\n                    [post_date_gmt] => 2024-07-04 04:20:49\n                    [post_content] => \n                    [post_title] => LOCALIZER\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => localizer\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-07-11 09:30:25\n                    [post_modified_gmt] => 2024-07-11 07:30:25\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25471\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n      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0.0012619495391846-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1119 level0\"><!-- Div Category --><div id=\"proteins\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Proteins<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/deepmind\/alphafold\" id=\"link-24913\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlphaFold<\/a>\n<!-- Time to render name section of link id 24913: 3.0994415283203E-6 --> \n<\/td>\n<td><p>AlphaFold is an AI system developed by DeepMind that predicts a protein\u2019s 3D structure from its amino acid sequence.<\/p>\n<!-- Time to render link large description section of link id 24913: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AlphaFold> How to use <\/a>\n<!-- Time to render notes section of link id 24913: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24913: 0.00018811225891113 --> \n<tr><td><a href=\"https:\/\/github.com\/BioComputingUP\/AlphaFold-disorder\" id=\"link-25668\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AlphaFold-disorder<\/a>\n<!-- Time to render name section of link id 25668: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Predict disorder and disorder binding from AlphaFold structures.<\/p>\n<!-- Time to render link large description section of link id 25668: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AlphaFold-disorder> How to use <\/a>\n<!-- Time to render notes section of link id 25668: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25668: 0.00017786026000977 --> \n<tr><td><a href=\"https:\/\/github.com\/lucidrains\/alphafold2\" id=\"link-24137\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Alphafold2-Pytorch<\/a>\n<!-- Time to render name section of link id 24137: 2.8610229492188E-6 --> \n<\/td>\n<td><p>An unofficial working Pytorch implementation of Alphafold2, a 3D protein predictor.<\/p>\n<!-- Time to render link large description section of link id 24137: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24137: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24137: 0.00012588500976562 --> \n<tr><td><a href=\"https:\/\/github.com\/sjdv1982\/attract\" id=\"link-25705\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ATTRACT<\/a>\n<!-- Time to render name section of link id 25705: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ATTRACT program suite for macromolecular docking (protein-protein, protein-nucleic acid, protein-peptide).<\/p>\n<!-- Time to render link large description section of link id 25705: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ATTRACT> How to use <\/a>\n<!-- Time to render notes section of link id 25705: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25705: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/BioComputingUP\/CAID\" id=\"link-25271\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CAID<\/a>\n<!-- Time to render name section of link id 25271: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The CAID software produces all outputs necessary for Critical Assessment of Intrinsic Disorder (CAID) edition, including baselines, references, metrics and plots, starting from predictions and a reference (see Data Availability section to know how to obtain this data).<\/p>\n<!-- Time to render link large description section of link id 25271: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CAID> How to use <\/a>\n<!-- Time to render notes section of link id 25271: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25271: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/Hoohm\/CITE-seq-Count\" id=\"link-24180\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CITE-seq-Count<\/a>\n<!-- Time to render name section of link id 24180: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool that allows to get UMI counts from a single cell protein assay.<\/p>\n<!-- Time to render link large description section of link id 24180: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24180: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24180: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/sokrypton\/ColabFold\" id=\"link-24900\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ColabFold<\/a>\n<!-- Time to render name section of link id 24900: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ColabFold is an easy-to-use Notebook based environment for fast and convenient protein structure predictions. Its structure prediction is powered by AlphaFold2 and RoseTTAFold combined with a fast multiple sequence alignment generation stage using MMseqs2.<\/p>\n<!-- Time to render link large description section of link id 24900: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ColabFold> How to use <\/a>\n<!-- Time to render notes section of link id 24900: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24900: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/dtu.biolib.com\/DeepTMHMM\" id=\"link-26224\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepTMHMM<\/a>\n<!-- Time to render name section of link id 26224: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Deep Learning Model for Transmembrane Topology Prediction and Classification<\/p>\n<!-- Time to render link large description section of link id 26224: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DeepTMHMM> How to use <\/a>\n<!-- Time to render notes section of link id 26224: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26224: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/bbuchfink\/diamond\" id=\"link-23798\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIAMOND<\/a>\n<!-- Time to render name section of link id 23798: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Accelerated BLAST compatible local sequence aligner.<\/p>\n<!-- Time to render link large description section of link id 23798: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DIAMOND> How to use <\/a>\n<!-- Time to render notes section of link id 23798: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23798: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/gcorso\/DiffDock\" id=\"link-26162\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DiffDock<\/a>\n<!-- Time to render name section of link id 26162: 2.1457672119141E-6 --> \n<\/td>\n<td><p>DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. Original paper on arXiv Implementation of DiffDock, state-of-the-art method for molecular docking, by Gabriele Corso*, Hannes Stark*, Bowen Jing*, Regina Barzilay and Tommi Jaakkola.<\/p>\n<!-- Time to render link large description section of link id 26162: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DiffDock> How to use <\/a>\n<!-- Time to render notes section of link id 26162: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26162: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/niuwa2333\/DTVF\" id=\"link-26173\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DTVF<\/a>\n<!-- Time to render name section of link id 26173: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Virulence Factor Prediction using Deep Learning.<\/p>\n<!-- Time to render link large description section of link id 26173: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DTVF> How to use <\/a>\n<!-- Time to render notes section of link id 26173: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26173: 0.00012421607971191 --> \n<tr><td><a href=\"https:\/\/github.com\/carnegie\/E2P2\" id=\"link-25295\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">E2P2<\/a>\n<!-- Time to render name section of link id 25295: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Ensemble Enzyme Prediction Pipeline.<\/p>\n<!-- Time to render link large description section of link id 25295: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_E2P2> How to use <\/a>\n<!-- Time to render notes section of link id 25295: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25295: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/egapx\" id=\"link-25748\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EGAPx<\/a>\n<!-- Time to render name section of link id 25748: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EGAPx is the publicly accessible version of the updated NCBI Eukaryotic Genome Annotation Pipeline.<\/p>\n<!-- Time to render link large description section of link id 25748: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EGAPx> How to use <\/a>\n<!-- Time to render notes section of link id 25748: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25748: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/kWeissenow\/EMBER3D\" id=\"link-24920\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMBER3D<\/a>\n<!-- Time to render name section of link id 24920: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Ultra-fast in-silico structure mutation.<\/p>\n<!-- Time to render link large description section of link id 24920: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMBER3D> How to use <\/a>\n<!-- Time to render notes section of link id 24920: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24920: 0.00017380714416504 --> \n<tr><td><a href=\"https:\/\/github.com\/OATML\/EVE\" id=\"link-25330\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EVE<\/a>\n<!-- Time to render name section of link id 25330: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EVE is a set of protein-specific models providing for any single amino acid mutation of interest a score reflecting the propensity of the resulting protein to be pathogenic.<\/p>\n<!-- Time to render link large description section of link id 25330: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EVE> How to use <\/a>\n<!-- Time to render notes section of link id 25330: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25330: 0.00010490417480469 --> \n<tr><td><a href=\"https:\/\/github.com\/patrickbryant1\/EvoBind\" id=\"link-25625\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EvoBind<\/a>\n<!-- Time to render name section of link id 25625: 9.5367431640625E-7 --> \n<\/td>\n<td><p>EvoBind (v2) designs novel peptide binders based only on a protein target sequence. It is not necessary to specify any target residues within the protein sequence or the length of the binder (although this is possible). Cyclic binder design is also possible.<\/p>\n<!-- Time to render link large description section of link id 25625: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EvoBind> How to use <\/a>\n<!-- Time to render notes section of link id 25625: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25625: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/danny-wilson\/genomegaMap\" id=\"link-25340\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">genomegaMap<\/a>\n<!-- Time to render name section of link id 25340: 1.9073486328125E-6 --> \n<\/td>\n<td>Within-species genome-wide dN\/dS estimation from very many genomes.\n<!-- Time to render link large description section of link id 25340: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_genomegaMap> How to use <\/a>\n<!-- Time to render notes section of link id 25340: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25340: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/cmbi\/hssp\" id=\"link-25667\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">hssp<\/a>\n<!-- Time to render name section of link id 25667: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Create DSSP and HSSP files. A series of PDB-related databanks for everyday needs.<\/p>\n<!-- Time to render link large description section of link id 25667: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_hssp> How to use <\/a>\n<!-- Time to render notes section of link id 25667: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25667: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/www.ebi.ac.uk\/interpro\/interproscan.html\" id=\"link-23649\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">InterProScan<\/a>\n<!-- Time to render name section of link id 23649: 2.1457672119141E-6 --> \n<\/td>\n<td><div>InterProScan is a tool that combines different protein signature recognition methods into one resource. No less than 14 pattern\/profiles databanks can be interrogated.<\/div>\n<!-- Time to render link large description section of link id 23649: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_InterProScan> How to use <\/a>\n<!-- Time to render notes section of link id 23649: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23649: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/JanaSperschneider\/LOCALIZER\" id=\"link-25471\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LOCALIZER<\/a>\n<!-- Time to render name section of link id 25471: 2.1457672119141E-6 --> \n<\/td>\n<td><p>LOCALIZER is a machine learning method for predicting the subcellular localization of both plant proteins and pathogen effectors in the plant cell.<\/p>\n<!-- Time to render link large description section of link id 25471: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LOCALIZER> How to use <\/a>\n<!-- Time to render notes section of link id 25471: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25471: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/Rostlab\/LocTree3\" id=\"link-23796\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Loctree3<\/a>\n<!-- Time to render name section of link id 23796: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Protein Subcelullar Localization Sequenced-Based Predictor<\/p>\n<!-- Time to render link large description section of link id 23796: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LocTree> How to use <\/a>\n<!-- Time to render notes section of link id 23796: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23796: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/pbwww.services.came.sbg.ac.at\/?page_id=416\" id=\"link-25154\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAESTRO<\/a>\n<!-- Time to render name section of link id 25154: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A Multi AgEnt STability pRedictiOn tool for changes in unfolding free energy upon point mutation.<\/p>\r\n<p>MAESTRO is structure based and distinguishes from similar approaches in the following points: (i) MAESTRO implements a multi-agent machine learning system. (ii) It provides predicted \u0394\u0394G values along with a corresponding prediction quality measure. (iii) MAESTRO is applicable to biological assemblies. (iv) It provides high throughput scanning for multi-point mutations where sites and types of mutation can be comprehensively controlled. (v) Finally, the software provides a specific mode for the prediction of stabilizing disulfide bonds.<\/p>\n<!-- Time to render link large description section of link id 25154: 3.814697265625E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAESTRO> How to use <\/a>\n<!-- Time to render notes section of link id 25154: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25154: 0.00012922286987305 --> \n<tr><td><a href=\"https:\/\/www.stavrox.com\/\" id=\"link-25970\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MeroX<\/a>\n<!-- Time to render name section of link id 25970: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MeroX is based on StavroX. It is specialized for cleavable cross-linkers. In addition to peptide backbone fragments, MeroX identifies cross-linker specific fragments in MS-MS data.<\/p>\n<!-- Time to render link large description section of link id 25970: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MeroX> How to use <\/a>\n<!-- Time to render notes section of link id 25970: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25970: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/miniprot\" id=\"link-24385\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniprot<\/a>\n<!-- Time to render name section of link id 24385: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Aligning proteins to genomes with splicing and frameshift.<\/p>\n<!-- Time to render link large description section of link id 24385: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniprot> How to use <\/a>\n<!-- Time to render notes section of link id 24385: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24385: 9.9897384643555E-5 --> \n<tr><td><a href=\"http:\/\/mzmine.github.io\" id=\"link-25243\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MZmine<\/a>\n<!-- Time to render name section of link id 25243: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MZmine is an open-source software for mass-spectrometry data processing.<\/p>\n<!-- Time to render link large description section of link id 25243: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MZmine> How to use <\/a>\n<!-- Time to render notes section of link id 25243: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25243: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/omabrowser.org\/standalone\/\" id=\"link-24753\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OMA<\/a>\n<!-- Time to render name section of link id 24753: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The OMA (Orthologous MAtrix) database is a well-established resource for identifying orthologs among publicly available complete genomes.<\/p>\n<!-- Time to render link large description section of link id 24753: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OMA> How to use <\/a>\n<!-- Time to render notes section of link id 24753: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24753: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/DessimozLab\/OMArk\" id=\"link-25541\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OMArk<\/a>\n<!-- Time to render name section of link id 25541: 1.9073486328125E-6 --> \n<\/td>\n<td><p>OMArk is a software for proteome (protein-coding gene repertoire) quality assessment.<\/p>\n<!-- Time to render link large description section of link id 25541: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OMArk> How to use <\/a>\n<!-- Time to render notes section of link id 25541: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25541: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/aqlaboratory\/openfold-3\" id=\"link-26159\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Openfold3<\/a>\n<!-- Time to render name section of link id 26159: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fully open source biomolecular structure prediction model based on AlphaFold3.<\/p>\n<!-- Time to render link large description section of link id 26159: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Openfold3> How to use <\/a>\n<!-- Time to render notes section of link id 26159: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26159: 9.7036361694336E-5 --> \n<tr><td><a href=\"https:\/\/orthologer.ezlab.org\/#getting-orthologer-software\" id=\"link-24775\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OrthoLoger<\/a>\n<!-- Time to render name section of link id 24775: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Standalone pipeline for delineation of orthologs.<\/p>\n<!-- Time to render link large description section of link id 24775: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24775: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24775: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/orthomcl.org\" id=\"link-24681\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OrthoMCL<\/a>\n<!-- Time to render name section of link id 24681: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.<\/p>\n<!-- Time to render link large description section of link id 24681: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OrthoMCL> How to use <\/a>\n<!-- Time to render notes section of link id 24681: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24681: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/pantools.readthedocs.io\/en\/latest\/\" id=\"link-25000\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanTools<\/a>\n<!-- Time to render name section of link id 25000: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PanTools is a toolkit for comparative analysis of large number of genomes.<\/p>\n<!-- Time to render link large description section of link id 25000: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanTools> How to use <\/a>\n<!-- Time to render notes section of link id 25000: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25000: 0.00011992454528809 --> \n<tr><td><a href=\"ftp:\/\/ftp.ebi.ac.uk\/pub\/databases\/Pfam\/Tools\/\" id=\"link-24437\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PfamScan<\/a>\n<!-- Time to render name section of link id 24437: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A program that searches a FASTA file against a library of Pfam HMMs.<\/p>\n<!-- Time to render link large description section of link id 24437: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PfamScan> How to use <\/a>\n<!-- Time to render notes section of link id 24437: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24437: 0.00012087821960449 --> \n<tr><td><a href=\"http:\/\/phobius.sbc.su.se\/index.html\" id=\"link-23956\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Phobius<\/a>\n<!-- Time to render name section of link id 23956: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A combined transmembrane topology and signal peptide predictor.<\/p>\n<!-- Time to render link large description section of link id 23956: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23956: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23956: 0.00011920928955078 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/plass\" id=\"link-24703\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Plass<\/a>\n<!-- Time to render name section of link id 24703: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.<\/p>\n<!-- Time to render link large description section of link id 24703: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24703: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24703: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/paulklemm_PHD\/proteinortho\" id=\"link-25229\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Proteinortho<\/a>\n<!-- Time to render name section of link id 25229: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Proteinortho is a tool to detect orthologous genes within different species.<\/p>\n<!-- Time to render link large description section of link id 25229: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Proteinortho> How to use <\/a>\n<!-- Time to render notes section of link id 25229: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25229: 9.0837478637695E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/gatech-genemark\/ProtHint\" id=\"link-24464\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProtHint<\/a>\n<!-- Time to render name section of link id 24464: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.<\/p>\n<!-- Time to render link large description section of link id 24464: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ProtHint> How to use <\/a>\n<!-- Time to render notes section of link id 24464: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24464: 9.7036361694336E-5 --> \n<tr><td><a href=\"http:\/\/provean.jcvi.org\" id=\"link-24465\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROVEAN<\/a>\n<!-- Time to render name section of link id 24465: 9.5367431640625E-7 --> \n<\/td>\n<td><p>PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.<\/p>\n<!-- Time to render link large description section of link id 24465: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PROVEAN> How to use <\/a>\n<!-- Time to render notes section of link id 24465: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24465: 9.608268737793E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/RosettaCommons\/RFdiffusion\" id=\"link-26170\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RFdiffusion<\/a>\n<!-- Time to render name section of link id 26170: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc).<\/p>\n<!-- Time to render link large description section of link id 26170: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RFdiffusion> How to use <\/a>\n<!-- Time to render notes section of link id 26170: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26170: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/pypi.org\/project\/seqconverter\" id=\"link-26169\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqconverter<\/a>\n<!-- Time to render name section of link id 26169: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The command-line program seqconverter can read and write text files containing aligned or unaligned DNA or protein sequences.<\/p>\n<!-- Time to render link large description section of link id 26169: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqconverter> How to use <\/a>\n<!-- Time to render notes section of link id 26169: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26169: 0.00014901161193848 --> \n<tr><td><a href=\"http:\/\/www.cbs.dtu.dk\/services\/SignalP\/\" id=\"link-23729\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SignalP<\/a>\n<!-- Time to render name section of link id 23729: 2.1457672119141E-6 --> \n<\/td>\n<td><div>SignalP 4.0 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.<\/div>\n<!-- Time to render link large description section of link id 23729: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SignalP> How to use <\/a>\n<!-- Time to render notes section of link id 23729: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23729: 9.5844268798828E-5 --> \n<tr><td><a href=\"http:\/\/www.cbs.dtu.dk\/cgi-bin\/nph-sw_request?tmhmm\" id=\"link-23767\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TMHMM<\/a>\n<!-- Time to render name section of link id 23767: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Prediction of transmembrane helices in proteins.<\/p>\n<!-- Time to render link large description section of link id 23767: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TMHMM> How to use <\/a>\n<!-- Time to render notes section of link id 23767: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23767: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/DeltaGroupNJUPT\/Vina-GPU-2.0\" id=\"link-26149\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vina-GPU-2.0<\/a>\n<!-- Time to render name section of link id 26149: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Vina-GPU 2.0 accelerates AutoDock Vina and its related commonly derived docking methods, such as QuickVina 2 and QuickVina-W with GPUs.<\/p>\n<!-- Time to render link large description section of link id 26149: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vina-GPU-2.0> How to use <\/a>\n<!-- Time to render notes section of link id 26149: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26149: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/XiaohuaZhangLLNL\/VinaLC\" id=\"link-25096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VinaLC<\/a>\n<!-- Time to render name section of link id 25096: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A parallel molecular docking program based on AutoDock Vina.<\/p>\n<!-- Time to render link large description section of link id 25096: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VinaLC> How to use <\/a>\n<!-- Time to render notes section of link id 25096: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25096: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/fmaguire\/WoLFPSort\" id=\"link-25469\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WoLFPSort<\/a>\n<!-- Time to render name section of link id 25469: 1.9073486328125E-6 --> \n<\/td>\n<td><p>WoLF PSORT is an extension of the PSORT II program for protein subcellular localization prediction, which is based on the PSORT principle. WoLF PSORT converts a protein's amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs.<\/p>\n<!-- Time to render link large description section of link id 25469: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WoLFPSort> How to use <\/a>\n<!-- Time to render notes section of link id 25469: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25469: 0.00011110305786133 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1121\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [field] => term_id\n                            [terms] => 1121\n                            [include_children] => \n                        )\n\n                )\n\n            [post_status] => Array\n                (\n                    [0] => publish\n                )\n\n            [orderby] => Array\n                (\n                    [title] => ASC\n                )\n\n        )\n\n    [query_vars] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => -1\n            [tax_query] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [field] => term_id\n                            [terms] => 1121\n                            [include_children] => \n                        )\n\n                )\n\n            [post_status] => Array\n                (\n                    [0] => publish\n                )\n\n            [orderby] => Array\n                (\n                    [title] => ASC\n                )\n\n            [error] => \n            [m] => \n            [p] => 0\n            [post_parent] => \n            [subpost] => \n            [subpost_id] => \n            [attachment] => \n            [attachment_id] => 0\n            [name] => \n            [pagename] => \n            [page_id] => 0\n            [second] => \n            [minute] => \n            [hour] => \n  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=> 1\n            [nopaging] => 1\n            [comments_per_page] => 50\n            [no_found_rows] => \n            [taxonomy] => link_library_category\n            [term_id] => 1121\n            [order] => DESC\n        )\n\n    [tax_query] => WP_Tax_Query Object\n        (\n            [queries] => Array\n                (\n                    [0] => Array\n                        (\n                            [taxonomy] => link_library_category\n                            [terms] => Array\n                                (\n                                    [0] => 1121\n                                )\n\n                            [field] => term_id\n                            [operator] => IN\n                            [include_children] => \n                        )\n\n                )\n\n            [relation] => AND\n            [table_aliases:protected] => Array\n                (\n                    [0] => wp_term_relationships\n                )\n\n            [queried_terms] => Array\n                (\n                    [link_library_category] => Array\n                        (\n                            [terms] => Array\n                                (\n                                    [0] => 1121\n                                )\n\n                            [field] => term_id\n                        )\n\n                )\n\n            [primary_table] => wp_posts\n            [primary_id_column] => ID\n        )\n\n    [meta_query] => WP_Meta_Query Object\n        (\n            [queries] => Array\n                (\n                )\n\n            [relation] => \n            [meta_table] => \n            [meta_id_column] => \n            [primary_table] => \n            [primary_id_column] => \n            [table_aliases:protected] => Array\n                (\n                )\n\n            [clauses:protected] => Array\n                (\n                )\n\n            [has_or_relation:protected] => \n        )\n\n    [date_query] => \n    [request] => \n\t\t\tSELECT   wp_posts.*\n\t\t\tFROM wp_posts  LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1121)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 25351\n                    [post_author] => 5\n                    [post_date] => 2024-04-22 15:06:18\n                    [post_date_gmt] => 2024-04-22 13:06:18\n                    [post_content] => \n                    [post_title] => 3rdChimeraMiner\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => 3rdchimeraminer\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-03 09:16:10\n                    [post_modified_gmt] => 2024-06-03 07:16:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25351\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 23579\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => AdapterRemoval\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => adapterremoval\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:21:18\n                    [post_modified_gmt] => 2025-05-21 05:21:18\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/adapterremoval\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 25570\n                    [post_author] => 5\n                    [post_date] => 2024-10-28 14:12:20\n                    [post_date_gmt] => 2024-10-28 13:12:20\n                    [post_content] => \n                    [post_title] => ALFATClust\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alfatclust\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-11-20 11:37:56\n                    [post_modified_gmt] => 2024-11-20 10:37:56\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25570\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 23585\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => Ampliconnoise\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => ampliconnoise\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:24:45\n                    [post_modified_gmt] => 2025-05-21 05:24:45\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/ampliconnoise\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [4] => WP_Post Object\n                (\n                    [ID] => 23874\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:41\n                    [post_date_gmt] => 2022-11-22 09:25:41\n                    [post_content] => \n                    [post_title] => atac dnase pipelines\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => atac-dnase-pipelines\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:30:04\n                    [post_modified_gmt] => 2025-05-21 05:30:04\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/atac-dnase-pipelines\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [5] => WP_Post Object\n                (\n                    [ID] => 24313\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:12\n                    [post_date_gmt] => 2022-11-22 09:26:12\n                    [post_content] => \n                    [post_title] => ATLAS\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => atlas-3\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:30:17\n                    [post_modified_gmt] => 2025-05-21 05:30:17\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/atlas-3\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [6] => WP_Post Object\n                (\n                    [ID] => 23969\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:45\n                    [post_date_gmt] => 2022-11-22 09:25:45\n                    [post_content] => \n                    [post_title] => Atropos\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => atropos\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:30:26\n                    [post_modified_gmt] => 2025-05-21 05:30:26\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/atropos\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [7] => WP_Post Object\n                (\n                    [ID] => 24157\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:00\n                    [post_date_gmt] => 2022-11-22 09:26:00\n                    [post_content] => \n                    [post_title] => BCOOL\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bcool\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:35:51\n                    [post_modified_gmt] => 2025-05-21 05:35:51\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bcool\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [8] => WP_Post Object\n                (\n                    [ID] => 26097\n                    [post_author] => 5\n                    [post_date] => 2025-09-16 06:35:57\n                    [post_date_gmt] => 2025-09-16 04:35:57\n                    [post_content] => \n                    [post_title] => biastools\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => biastools\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-12-17 13:50:56\n                    [post_modified_gmt] => 2025-12-17 12:50:56\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26097\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [9] => WP_Post Object\n                (\n                    [ID] => 24125\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:52\n                    [post_date_gmt] => 2022-11-22 09:25:52\n                    [post_content] => \n                    [post_title] => Btrim\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => btrim\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:42:10\n                    [post_modified_gmt] => 2025-05-21 05:42:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/btrim\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [10] => WP_Post Object\n                (\n                    [ID] => 24175\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:11\n                    [post_date_gmt] => 2022-11-22 09:26:11\n                    [post_content] => \n                    [post_title] => charcoal\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => charcoal\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:08:04\n                    [post_modified_gmt] => 2025-05-21 06:08:04\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/charcoal\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 25590\n                    [post_author] => 5\n                    [post_date] => 2024-12-03 07:11:52\n                    [post_date_gmt] => 2024-12-03 06:11:52\n                    [post_content] => \n                    [post_title] => CheckM2\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => checkm2\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-12-18 09:48:25\n                    [post_modified_gmt] => 2024-12-18 08:48:25\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25590\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [12] => WP_Post Object\n                (\n                    [ID] => 24603\n                    [post_author] => 5\n                    [post_date] => 2022-11-23 13:12:56\n                    [post_date_gmt] => 2022-11-23 12:12:56\n                    [post_content] => \n                    [post_title] => CheckV\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => checkv\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:08:10\n                    [post_modified_gmt] => 2025-05-21 06:08:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24603\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [13] => WP_Post Object\n                (\n                    [ID] => 25324\n                    [post_author] => 5\n                    [post_date] => 2024-03-25 10:29:02\n                    [post_date_gmt] => 2024-03-25 09:29:02\n                    [post_content] => \n                    [post_title] => chopper\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => chopper\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-28 14:00:35\n                    [post_modified_gmt] => 2024-03-28 13:00:35\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25324\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [14] => WP_Post Object\n                (\n                    [ID] => 24077\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:50\n                    [post_date_gmt] => 2022-11-22 09:25:50\n                    [post_content] => \n                    [post_title] => ClipAndMerge\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => clipandmerge\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:11:11\n                    [post_modified_gmt] => 2025-05-21 06:11:11\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/clipandmerge\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n          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[menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [16] => WP_Post Object\n                (\n                    [ID] => 24185\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:06\n                    [post_date_gmt] => 2022-11-22 09:26:06\n                    [post_content] => \n                    [post_title] => Consensify\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => consensify\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:13:32\n                    [post_modified_gmt] => 2025-05-21 06:13:32\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/consensify\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [17] => WP_Post Object\n                (\n                    [ID] => 25416\n                    [post_author] => 5\n                    [post_date] => 2024-05-23 09:14:22\n                    [post_date_gmt] => 2024-05-23 07:14:22\n                    [post_content] => \n                    [post_title] => ContScout\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => contscout\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-17 08:47:50\n                    [post_modified_gmt] => 2024-06-17 06:47:50\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25416\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [18] => WP_Post Object\n                (\n                    [ID] => 23900\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:42\n                    [post_date_gmt] => 2022-11-22 09:25:42\n                    [post_content] => \n                    [post_title] => CroCo\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => croco\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:15:03\n                    [post_modified_gmt] => 2025-05-21 06:15:03\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/croco\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [19] => WP_Post Object\n                (\n                    [ID] => 23611\n            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Execution Time: 0.0020918846130371-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1121 level0\"><!-- Div Category --><div id=\"quality-and-cleaning\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Quality and cleaning<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/dulunar\/3rdChimeraMiner\" id=\"link-25351\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">3rdChimeraMiner<\/a>\n<!-- Time to render name section of link id 25351: 1.9073486328125E-6 --> \n<\/td>\n<td>Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.\n<!-- Time to render link large description section of link id 25351: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_3rdChimeraMiner> How to use <\/a>\n<!-- Time to render notes section of link id 25351: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25351: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/MikkelSchubert\/adapterremoval\" id=\"link-23579\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AdapterRemoval<\/a>\n<!-- Time to render name section of link id 23579: 9.0599060058594E-6 --> \n<\/td>\n<td><p>This program was developed to remove residual adapter sequences from next generation sequencing reads. The program handles both single end and paired end data.<\/p>\n<!-- Time to render link large description section of link id 23579: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AdapterRemoval> How to use <\/a>\n<!-- Time to render notes section of link id 23579: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23579: 0.00013899803161621 --> \n<tr><td><a href=\"https:\/\/github.com\/phglab\/ALFATClust\" id=\"link-25570\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ALFATClust<\/a>\n<!-- Time to render name section of link id 25570: 9.5367431640625E-7 --> \n<\/td>\n<td>ALignment-Free Adaptive Threshold Clustering:Biological sequence clustering tool with dynamic threshold for individual clusters. Suitable for clustering multiple groups of homologous sequences.\n<!-- Time to render link large description section of link id 25570: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ALFATClust> How to use <\/a>\n<!-- Time to render notes section of link id 25570: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25570: 9.9897384643555E-5 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/ampliconnoise\/\" id=\"link-23585\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ampliconnoise<\/a>\n<!-- Time to render name section of link id 23585: 2.1457672119141E-6 --> \n<\/td>\n<td><p>AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal.<\/p>\n<!-- Time to render link large description section of link id 23585: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23585: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23585: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/kundajelab\/atac_dnase_pipelines\" id=\"link-23874\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">atac dnase pipelines<\/a>\n<!-- Time to render name section of link id 23874: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ATAC-seq and DNase-seq processing pipeline. This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data.<\/p>\n<!-- Time to render link large description section of link id 23874: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23874: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23874: 0.0001218318939209 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/wegmannlab\/atlas\/wiki\/Home\" id=\"link-24313\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ATLAS<\/a>\n<!-- Time to render name section of link id 24313: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ATLAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file. There are sequence data processing tools, diagnostic tools, and variant discovery tools, similar to GATK by the Broad Institute.<\/p>\n<!-- Time to render link large description section of link id 24313: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ATLAS> How to use <\/a>\n<!-- Time to render notes section of link id 24313: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24313: 0.00018906593322754 --> \n<tr><td><a href=\"https:\/\/github.com\/jdidion\/atropos\" id=\"link-23969\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Atropos<\/a>\n<!-- Time to render name section of link id 23969: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of Cutadapt read trimmer.<\/p>\n<!-- Time to render link large description section of link id 23969: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23969: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23969: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/Malfoy\/BCOOL\" id=\"link-24157\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BCOOL<\/a>\n<!-- Time to render name section of link id 24157: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BCOOL is a read corrector for NGS sequencing data that align reads on a de Bruijn graph.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24157: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24157: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24157: 0.00010108947753906 --> \n<tr><td><a href=\"https:\/\/github.com\/maojanlin\/biastools\" id=\"link-26097\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">biastools<\/a>\n<!-- Time to render name section of link id 26097: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The toolkits to analyze reference bias of short DNA read alignment.<\/p>\n<!-- Time to render link large description section of link id 26097: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_biastools> How to use <\/a>\n<!-- Time to render notes section of link id 26097: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26097: 0.00018405914306641 --> \n<tr><td><a href=\"http:\/\/graphics.med.yale.edu\/trim\/\" id=\"link-24125\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Btrim<\/a>\n<!-- Time to render name section of link id 24125: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and accurate adapter, barcodes, and low-quality region trimming and binning program written in C for next-generating sequencing reads. The search algorithm is based on Eugene Myers' fast bit-vector algorithm.<\/p>\n<!-- Time to render link large description section of link id 24125: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24125: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24125: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/dib-lab\/charcoal\" id=\"link-24175\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">charcoal<\/a>\n<!-- Time to render name section of link id 24175: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Remove contaminated contigs from genomes using k-mers and taxonomies.<\/p>\n<!-- Time to render link large description section of link id 24175: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24175: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24175: 0.00019216537475586 --> \n<tr><td><a href=\"https:\/\/github.com\/chklovski\/CheckM2\" id=\"link-25590\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CheckM2<\/a>\n<!-- Time to render name section of link id 25590: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Assessing the quality of metagenome-derived genome bins using machine learning.<\/p>\n<!-- Time to render link large description section of link id 25590: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CheckM2> How to use <\/a>\n<!-- Time to render notes section of link id 25590: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25590: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/berkeleylab\/checkv\/src\/master\/\" id=\"link-24603\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CheckV<\/a>\n<!-- Time to render name section of link id 24603: 2.8610229492188E-6 --> \n<\/td>\n<td><p>CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.<\/p>\n<!-- Time to render link large description section of link id 24603: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24603: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24603: 0.00021696090698242 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/chopper\" id=\"link-25324\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chopper<\/a>\n<!-- Time to render name section of link id 25324: 3.0994415283203E-6 --> \n<\/td>\n<td><p>This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.<\/p>\r\n<p>chopper is a tool that reunites the now outdated softwares NanoFilt and NanoLyse. It permits to filter QC files and has a faster execution time than NanoFilt and NanoLyse.<\/p>\r\n<p>&nbsp;<\/p>\n<!-- Time to render link large description section of link id 25324: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chopper> How to use <\/a>\n<!-- Time to render notes section of link id 25324: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25324: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/apeltzer\/ClipAndMerge\" id=\"link-24077\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClipAndMerge<\/a>\n<!-- Time to render name section of link id 24077: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Clip&amp;Merge is a tool to clip off adapters from sequencing reads and merge overlapping paired end reads together.<\/p>\n<!-- Time to render link large description section of link id 24077: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClipAndMerge> How to use <\/a>\n<!-- Time to render notes section of link id 24077: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24077: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/huangnengCSU\/compleasm\" id=\"link-25251\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">compleasm<\/a>\n<!-- Time to render name section of link id 25251: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A genome completeness evaluation tool based on miniprot.<\/p>\n<!-- Time to render link large description section of link id 25251: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_compleasm> How to use <\/a>\n<!-- Time to render notes section of link id 25251: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25251: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/jlapaijmans\/Consensify\" id=\"link-24185\" class=\"track_this_link \" rel=\"noopener noreferrer\">Consensify<\/a>\n<!-- Time to render name section of link id 24185: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to standard pseudohaploidisation.<\/p>\n<!-- Time to render link large description section of link id 24185: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24185: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24185: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/h836472\/ContScout\" id=\"link-25416\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ContScout<\/a>\n<!-- Time to render name section of link id 25416: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ContScout is a pipeline developed for the identification and removal of contaminating sequences in draft genomes.<\/p>\n<!-- Time to render link large description section of link id 25416: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ContScout> How to use <\/a>\n<!-- Time to render notes section of link id 25416: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25416: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/gitlab.mbb.univ-montp2.fr\/mbb\/CroCo\" id=\"link-23900\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CroCo<\/a>\n<!-- Time to render name section of link id 23900: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification.<\/p>\n<!-- Time to render link large description section of link id 23900: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23900: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23900: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/cutadapt.readthedocs.io\/en\/stable\/\" id=\"link-23611\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cutadapt<\/a>\n<!-- Time to render name section of link id 23611: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.<\/p>\n<!-- Time to render link large description section of link id 23611: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cutadapt> How to use <\/a>\n<!-- Time to render notes section of link id 23611: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23611: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/LuoGroup2023\/DeChat\" id=\"link-25400\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeChat<\/a>\n<!-- Time to render name section of link id 25400: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.<\/p>\n<!-- Time to render link large description section of link id 25400: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DeChat> How to use <\/a>\n<!-- Time to render notes section of link id 25400: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25400: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/CamilaDuitama\/decOM\" id=\"link-25231\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">decOM<\/a>\n<!-- Time to render name section of link id 25231: 2.8610229492188E-6 --> \n<\/td>\n<td><p>decOM is a high-accuracy microbial source tracking method that is suitable for contamination quantification in paleogenomics, namely the analysis of collections of possibly contaminated ancient oral metagenomic data sets.<\/p>\n<!-- Time to render link large description section of link id 25231: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_decOM> How to use <\/a>\n<!-- Time to render notes section of link id 25231: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25231: 0.00011205673217773 --> \n<tr><td><a href=\"http:\/\/deconseq.sourceforge.net\/\" id=\"link-23878\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeconSeq<\/a>\n<!-- Time to render name section of link id 23878: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Detect and remove contaminations from your sequence data.<\/p>\n<!-- Time to render link large description section of link id 23878: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23878: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23878: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/apeltzer\/DeDup\" id=\"link-24196\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeDup<\/a>\n<!-- Time to render name section of link id 24196: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A merged read deduplication tool capable to perform merged read deduplication on single end data.<\/p>\n<!-- Time to render link large description section of link id 24196: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24196: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24196: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/ecopcr\/wikis\/home\" id=\"link-23616\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ecoPCR<\/a>\n<!-- Time to render name section of link id 23616: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ecoPCR is an electronic PCR software developed by LECAand Helix-Project . It helps you to estimate Barcode primers quality. In conjunction with OBItools, you can postprocess ecoPCR output to compute barcode coverage and barcode speci?city.<\/p>\n<!-- Time to render link large description section of link id 23616: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ecoPCR> How to use <\/a>\n<!-- Time to render notes section of link id 23616: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23616: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/ecoprimers\/wikis\/home\" id=\"link-23617\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ecoPrimers<\/a>\n<!-- Time to render name section of link id 23617: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ecoPrimer is a barcoding software which is written in C language. It finds universal primers from a set of input DNA sequences by finding conserved regions without \"a priori\" on candidate sequences. It also evaluates the quality of the primers and barcode regions by measuring the \"barcode specificity\" and \"barcode coverage\" indices<\/p>\n<!-- Time to render link large description section of link id 23617: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ecoPrimers> How to use <\/a>\n<!-- Time to render notes section of link id 23617: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23617: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/arshajii\/ema\" id=\"link-24211\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMA<\/a>\n<!-- Time to render name section of link id 24211: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EMA uses a latent variable model to align barcoded short-reads (such as those produced by 10x Genomics' sequencing platform).<\/p>\n<!-- Time to render link large description section of link id 24211: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24211: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24211: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/NBISweden\/EMBLmyGFF3\" id=\"link-26160\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMBLmyGFF3<\/a>\n<!-- Time to render name section of link id 26160: 2.1457672119141E-6 --> \n<\/td>\n<td><p>An efficient way to convert gff3 annotation files into EMBL format ready to submit.<\/p>\n<!-- Time to render link large description section of link id 26160: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMBLmyGFF3> How to use <\/a>\n<!-- Time to render notes section of link id 26160: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26160: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/fastix\" id=\"link-25004\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastix<\/a>\n<!-- Time to render name section of link id 25004: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A simple command line tool to add prefixes to FASTA headers.<\/p>\n<!-- Time to render link large description section of link id 25004: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastix> How to use <\/a>\n<!-- Time to render notes section of link id 25004: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25004: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/fastk-medians\" id=\"link-25442\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastk-medians<\/a>\n<!-- Time to render name section of link id 25442: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of utilities to calculate the median number of times the k-mers in a sequence of interest occur across the whole set.<\/p>\n<!-- Time to render link large description section of link id 25442: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastk-medians> How to use <\/a>\n<!-- Time to render notes section of link id 25442: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25442: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/OpenGene\/fastp\" id=\"link-23988\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastp<\/a>\n<!-- Time to render name section of link id 23988: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool designed to provide fast all-in-one preprocessing for FastQ files.<\/p>\n<!-- Time to render link large description section of link id 23988: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastp> How to use <\/a>\n<!-- Time to render notes section of link id 23988: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23988: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/OpenGene\/fastplong\" id=\"link-25596\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastplong<\/a>\n<!-- Time to render name section of link id 25596: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Ultra-fast preprocessing and quality control for long-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25596: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastplong> How to use <\/a>\n<!-- Time to render notes section of link id 25596: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25596: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastq_screen\/\" id=\"link-23834\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastQ Screen<\/a>\n<!-- Time to render name section of link id 23834: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.<\/p>\n<!-- Time to render link large description section of link id 23834: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastQScreen> How to use <\/a>\n<!-- Time to render notes section of link id 23834: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23834: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/cancan.cshl.edu\/labmembers\/gordon\/fastq_illumina_filter\/\" id=\"link-23894\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastq_illumina_filter<\/a>\n<!-- Time to render name section of link id 23894: 2.8610229492188E-6 --> \n<\/td>\n<td><p>This program can filter FASTQ files produced by CASAVA 1.8, and keep\/discard reads based on this filter flag.<\/p>\n<!-- Time to render link large description section of link id 23894: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fastq_illumina_filter> How to use <\/a>\n<!-- Time to render notes section of link id 23894: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23894: 0.00012588500976562 --> \n<tr><td><a href=\"https:\/\/homes.cs.washington.edu\/~dcjones\/fastq-tools\/\" id=\"link-24231\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastq-tools<\/a>\n<!-- Time to render name section of link id 24231: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.<\/p>\n<!-- Time to render link large description section of link id 24231: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24231: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24231: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/\" id=\"link-23624\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastQC<\/a>\n<!-- Time to render name section of link id 23624: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A Quality Control application for FastQ files. FastQC is an application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report.<\/p>\n<!-- Time to render link large description section of link id 23624: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastQC> How to use <\/a>\n<!-- Time to render notes section of link id 23624: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23624: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/statgen\/fastQValidator\" id=\"link-24122\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fastQValidator<\/a>\n<!-- Time to render name section of link id 24122: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The fastQValidator validates the format of fastq files<\/p>\n<!-- Time to render link large description section of link id 24122: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24122: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24122: 0.00012087821960449 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/fcs\" id=\"link-25990\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FCS<\/a>\n<!-- Time to render name section of link id 25990: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The NCBI Foreign Contamination Screen (FCS) is a tool suite (FCS-adaptator et FCS-gx) for identifying and removing contaminant sequences in genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 25990: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FCS> How to use <\/a>\n<!-- Time to render notes section of link id 25990: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25990: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/fcs-gx\" id=\"link-25536\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FCS-GX<\/a>\n<!-- Time to render name section of link id 25536: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FCS-GX detects contamination from foreign organisms in genome sequences. This tool is one module within the NCBI Foreign Contamination Screening (FCS) program suite.<\/p>\n<!-- Time to render link large description section of link id 25536: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FCS-GX> How to use <\/a>\n<!-- Time to render notes section of link id 25536: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25536: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Filtlong\" id=\"link-24232\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Filtlong<\/a>\n<!-- Time to render name section of link id 24232: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Filtlong is a tool for filtering long reads by quality.<\/p>\n<!-- Time to render link large description section of link id 24232: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Filtlong> How to use <\/a>\n<!-- Time to render notes section of link id 24232: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24232: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/baoe\/FLAS\" id=\"link-24096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAS<\/a>\n<!-- Time to render name section of link id 24096: 2.1457672119141E-6 --> \n<\/td>\n<td><p>FLAS is software that makes self-correction for PacBio long reads with fast speed and high throughput.<\/p>\n<!-- Time to render link large description section of link id 24096: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24096: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24096: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/seqan\/flexbar\" id=\"link-23630\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Flexbar<\/a>\n<!-- Time to render name section of link id 23630: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta\/q and csfasta\/q format from Illumina, Roche 454, and the SOLiD platform.<\/p>\n<!-- Time to render link large description section of link id 23630: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Flexbar> How to use <\/a>\n<!-- Time to render notes section of link id 23630: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23630: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/holtjma\/fmlrc\" id=\"link-24237\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FMLRC<\/a>\n<!-- Time to render name section of link id 24237: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24237: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24237: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24237: 0.0001220703125 --> \n<tr><td><a href=\"https:\/\/github.com\/rdpstaff\/Framebot\" id=\"link-23711\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FrameBot<\/a>\n<!-- Time to render name section of link id 23711: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RDP FrameBot is a tool for correcting frameshift errors caused by insertions and deletions in DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 23711: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23711: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23711: 0.00011920928955078 --> \n<tr><td><a href=\"https:\/\/github.com\/yeeus\/GCI.git\" id=\"link-25561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GCI<\/a>\n<!-- Time to render name section of link id 25561: 2.1457672119141E-6 --> \n<\/td>\n<td>Genome Continuity Inspector (GCI) is an assembly assessment tool for high-quality genomes (e.g. T2T genomes), in base resolution.\n<!-- Time to render link large description section of link id 25561: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCI> How to use <\/a>\n<!-- Time to render notes section of link id 25561: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25561: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/bacpop\/ggCaller\" id=\"link-25574\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ggCaller<\/a>\n<!-- Time to render name section of link id 25574: 1.9073486328125E-6 --> \n<\/td>\n<td>A de Bruijn graph-based gene-caller and pangenome analysis tool.\n<!-- Time to render link large description section of link id 25574: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ggCaller> How to use <\/a>\n<!-- Time to render notes section of link id 25574: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25574: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/kishwarshafin\/helen\" id=\"link-24284\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HELEN<\/a>\n<!-- Time to render name section of link id 24284: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HELEN (Homopolymer Encoded Long-read Error-corrector for Nanopore) uses a Recurrent-Neural-Network (RNN) based Multi-Task Learning (MTL) model that can predict a base and a run-length for each genomic position using the weights generated by MarginPolish. This installation includes MarginPolish.<\/p>\n<!-- Time to render link large description section of link id 24284: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24284: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24284: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/morispi\/HG-CoLoR\" id=\"link-24044\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HG-CoLoR<\/a>\n<!-- Time to render name section of link id 24044: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HG-CoLoR (Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads) is a hybrid method for the error correction of long reads that both aligns the short reads to the long reads, and uses a variable-order de Bruijn graph, in a seed-and-extend approach.<\/p>\n<!-- Time to render link large description section of link id 24044: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24044: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24044: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/sheinasim\/HiFiAdapterFilt\" id=\"link-24291\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HiFiAdapterFilt<\/a>\n<!-- Time to render name section of link id 24291: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences.<\/p>\n<!-- Time to render link large description section of link id 24291: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HiFiAdapterFilt> How to use <\/a>\n<!-- Time to render notes section of link id 24291: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24291: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/ChongLab\/Inspector\" id=\"link-24299\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">Inspector<\/a>\n<!-- Time to render name section of link id 24299: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for evaluate long-read de novo assembly results.<\/p>\n<!-- Time to render link large description section of link id 24299: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Inspector> How to use <\/a>\n<!-- Time to render notes section of link id 24299: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24299: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/USDA-ARS-GBRU\/itsxpress\" id=\"link-25732\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ITSxpress<\/a>\n<!-- Time to render name section of link id 25732: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis.<\/p>\n<!-- Time to render link large description section of link id 25732: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ITSxpress> How to use <\/a>\n<!-- Time to render notes section of link id 25732: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25732: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/biointec\/jabba\" id=\"link-24329\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jabba<\/a>\n<!-- Time to render name section of link id 24329: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A hybrid error correction tool for sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24329: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24329: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24329: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/liu3zhenlab\/kad\" id=\"link-24335\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KAD<\/a>\n<!-- Time to render name section of link id 24335: 2.1457672119141E-6 --> \n<\/td>\n<td><p>KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies.<\/p>\n<!-- Time to render link large description section of link id 24335: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24335: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24335: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/www.earlham.ac.uk\/kat-tools\" id=\"link-23955\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KAT<\/a>\n<!-- Time to render name section of link id 23955: 2.1457672119141E-6 --> \n<\/td>\n<td><p>KAT (The K-mer Analysis Toolkit) is a suite of tools that generate, analyse and compare k-mer spectra produced from sequence files.<\/p>\n<!-- Time to render link large description section of link id 23955: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KAT> How to use <\/a>\n<!-- Time to render notes section of link id 23955: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23955: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/kcoss-2021\/KCOSS\" id=\"link-24742\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KCOSS<\/a>\n<!-- Time to render name section of link id 24742: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and space-saving multi-threaded k-mer frequency statistics algorithm<\/p>\n<!-- Time to render link large description section of link id 24742: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24742: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24742: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/catchenlab.life.illinois.edu\/klumpy\/\" id=\"link-26205\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">klumpy<\/a>\n<!-- Time to render name section of link id 26205: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Klumpy is a bioinformatic tool for identifying possibly incorrectly assembled regions in a long-read based assembly, with the additional capabilities of annotating sequences given a set of query sequences.<\/p>\n<!-- Time to render link large description section of link id 26205: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_klumpy> How to use <\/a>\n<!-- Time to render notes section of link id 26205: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26205: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/kmer-counter\" id=\"link-25440\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kmer-counter<\/a>\n<!-- Time to render name section of link id 25440: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast k-mer counter written in Rust.<\/p>\n<!-- Time to render link large description section of link id 25440: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kmer-counter> How to use <\/a>\n<!-- Time to render notes section of link id 25440: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25440: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/eclarke\/komplexity\" id=\"link-24340\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">komplexity<\/a>\n<!-- Time to render name section of link id 24340: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A command-line tool built in Rust to quickly calculate and\/or mask low-complexity sequences from a FAST<A\/Q> file. This uses the number of unique k-mers over a sequence divided by the length to assess complexity.<\/p>\n<!-- Time to render link large description section of link id 24340: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_komplexity> How to use <\/a>\n<!-- Time to render notes section of link id 24340: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24340: 0.00012397766113281 --> \n<tr><td><a href=\"https:\/\/github.com\/yfukasawa\/LongQC\" id=\"link-24354\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LongQC<\/a>\n<!-- Time to render name section of link id 24354: 2.1457672119141E-6 --> \n<\/td>\n<td><p>LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc.<\/p>\n<!-- Time to render link large description section of link id 24354: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LongQC> How to use <\/a>\n<!-- Time to render notes section of link id 24354: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24354: 0.00011420249938965 --> \n<tr><td><a href=\"http:\/\/atgc.lirmm.fr\/lordec\/\" id=\"link-23657\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LoRDEC<\/a>\n<!-- Time to render name section of link id 23657: 2.1457672119141E-6 --> \n<\/td>\n<td><p>LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.<\/p>\n<!-- Time to render link large description section of link id 23657: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LoRDEC> How to use <\/a>\n<!-- Time to render notes section of link id 23657: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23657: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/ginolhac.github.io\/mapDamage\/\" id=\"link-23909\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mapDamage<\/a>\n<!-- Time to render name section of link id 23909: 1.9073486328125E-6 --> \n<\/td>\n<td><p>tracking and quantifying damage patterns in ancient DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 23909: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mapDamage> How to use <\/a>\n<!-- Time to render notes section of link id 23909: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23909: 0.00012803077697754 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/MECAT\" id=\"link-23979\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MECAT<\/a>\n<!-- Time to render name section of link id 23979: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads.<\/p>\n<!-- Time to render link large description section of link id 23979: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23979: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23979: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/nanoporetech\/medaka\" id=\"link-23989\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Medaka<\/a>\n<!-- Time to render name section of link id 23989: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Medaka demonstrates a framework for error correcting sequencing data, particularly aimed at nanopore sequencing. Tools are provided for both training and inference. The code exploits the keras deep learning library.<\/p>\n<!-- Time to render link large description section of link id 23989: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Medaka> How to use <\/a>\n<!-- Time to render notes section of link id 23989: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23989: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/roblanf\/minion_qc\" id=\"link-24383\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MinIONQC<\/a>\n<!-- Time to render name section of link id 24383: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast and effective quality control for MinION and PromethION sequencing data<\/p>\n<!-- Time to render link large description section of link id 24383: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24383: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24383: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/berkeleylab\/jgi-miniscrub\/src\/master\/\" id=\"link-24386\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiniScrub<\/a>\n<!-- Time to render name section of link id 24386: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MiniScrub is a de novo long sequencing read preprocessing method that improves read quality by predicting and removing (\"scrubbing\") read segments that have a high concentration of errors.<\/p>\n<!-- Time to render link large description section of link id 24386: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24386: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24386: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/linzhi2013\/MitoZ\" id=\"link-24392\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MitoZ<\/a>\n<!-- Time to render name section of link id 24392: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization.<\/p>\n<!-- Time to render link large description section of link id 24392: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MitoZ> How to use <\/a>\n<!-- Time to render notes section of link id 24392: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24392: 0.0001068115234375 --> \n<tr><td><a href=\"http:\/\/musket.sourceforge.net\/homepage.htm#latest\" id=\"link-24403\" class=\"track_this_link \" rel=\"noopener noreferrer\">Musket<\/a>\n<!-- Time to render name section of link id 24403: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing.<\/p>\n<!-- Time to render link large description section of link id 24403: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24403: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24403: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/PrestonLeung\/Nano-Q\" id=\"link-24405\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Nano-Q<\/a>\n<!-- Time to render name section of link id 24405: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Python script for conservatively cleaning ONT reads from bam files and estimate variant frequencies.<\/p>\n<!-- Time to render link large description section of link id 24405: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24405: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24405: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoComp\" id=\"link-23942\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoComp<\/a>\n<!-- Time to render name section of link id 23942: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Compare multiple runs of long read sequencing data and alignments.<\/p>\n<!-- Time to render link large description section of link id 23942: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> in Python-3.11.1\n<!-- Time to render notes section of link id 23942: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23942: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/nanofilt\" id=\"link-23857\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoFilt<\/a>\n<!-- Time to render name section of link id 23857: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Filtering and trimming of Oxford Nanopore sequencing data<\/p>\n<!-- Time to render link large description section of link id 23857: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23857: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23857: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoLyse\" id=\"link-23944\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoLyse<\/a>\n<!-- Time to render name section of link id 23944: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Remove reads mapping to the lambda phage genome from a fastq file<\/p>\n<!-- Time to render link large description section of link id 23944: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_nanolyse> How to use <\/a>\n<!-- Time to render notes section of link id 23944: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23944: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/wdecoster\/NanoStat\" id=\"link-23943\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoStat<\/a>\n<!-- Time to render name section of link id 23943: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Create statistic summary of an Oxford Nanopore read dataset<\/p>\n<!-- Time to render link large description section of link id 23943: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoStat> How to use <\/a>\n<!-- Time to render notes section of link id 23943: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23943: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/Nextomics\/NextPolish\" id=\"link-24415\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NextPolish<\/a>\n<!-- Time to render name section of link id 24415: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NextPolish is used to fix base errors (SNV\/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both.<\/p>\n<!-- Time to render link large description section of link id 24415: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NextPolish> How to use <\/a>\n<!-- Time to render notes section of link id 24415: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24415: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/clwgg\/nQuire\" id=\"link-24420\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">nQuire<\/a>\n<!-- Time to render name section of link id 24420: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A statistical framework for ploidy estimation using NGS short-read data.<\/p>\n<!-- Time to render link large description section of link id 24420: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_nQuire> How to use <\/a>\n<!-- Time to render notes section of link id 24420: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24420: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/DessimozLab\/OMArk\" id=\"link-25541\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">OMArk<\/a>\n<!-- Time to render name section of link id 25541: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OMArk is a software for proteome (protein-coding gene repertoire) quality assessment.<\/p>\n<!-- Time to render link large description section of link id 25541: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_OMArk> How to use <\/a>\n<!-- Time to render notes section of link id 25541: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25541: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/swarris\/Pacasus\" id=\"link-24006\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pacasus<\/a>\n<!-- Time to render name section of link id 24006: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Tool for detecting and cleaning PacBio \/ Nanopore long reads after whole genome amplification.<\/p>\n<!-- Time to render link large description section of link id 24006: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24006: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24006: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/gem-pasteur\/PanACoTA\" id=\"link-26201\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanACoTA<\/a>\n<!-- Time to render name section of link id 26201: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PANgenome with Annotations, COre identification, Tree and corresponding Alignments.<\/p>\n<!-- Time to render link large description section of link id 26201: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanACoTA> How to use <\/a>\n<!-- Time to render notes section of link id 26201: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26201: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/lemene\/PECAT\" id=\"link-25450\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PECAT<\/a>\n<!-- Time to render name section of link id 25450: 1.9073486328125E-6 --> \n<\/td>\n<td><p>PECAT is a phased error correction and assembly tool for long reads. It includes a haplotype-aware correction method and an efficient diploid assembly method.<\/p>\n<!-- Time to render link large description section of link id 25450: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PECAT> How to use <\/a>\n<!-- Time to render notes section of link id 25450: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25450: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/platanus.bio.titech.ac.jp\/pltanus_trim\" id=\"link-24454\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Platanus_trim<\/a>\n<!-- Time to render name section of link id 24454: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Platanus_trim is a tool for trimming adaptor sequences and low quality regions. In contrast, Platanus_internal_trim is a tool for trimming internal adaptor sequence, adaptor sequences, and low quality regions. Platanus_trim is designed for paired-end library and Platanus_internal_trim is for mate-pair library.<\/p>\n<!-- Time to render link large description section of link id 24454: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24454: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24454: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/rrwick\/Porechop#requirements\" id=\"link-23850\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Porechop<\/a>\n<!-- Time to render name section of link id 23850: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.<\/p>\n<!-- Time to render link large description section of link id 23850: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Porechop> How to use <\/a>\n<!-- Time to render notes section of link id 23850: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23850: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bonsai-team\/Porechop_ABI\" id=\"link-24099\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Porechop_ABI<\/a>\n<!-- Time to render name section of link id 24099: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Porechop_abi (ab initio) is an extension of Porechop that is able to infer the adapter sequence from the Oxford Nanopore reads. It discovers the adapter sequence from the reads using approximate k-mers and assembly, and add the sequence found to the adapter list (adapters.py file).<\/p>\n<!-- Time to render link large description section of link id 24099: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Porechop_ABI> How to use <\/a>\n<!-- Time to render notes section of link id 24099: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24099: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/prinseq.sourceforge.net\" id=\"link-24027\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PRINSEQ<\/a>\n<!-- Time to render name section of link id 24027: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.<\/p>\n<!-- Time to render link large description section of link id 24027: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PRINSEQ> How to use <\/a>\n<!-- Time to render notes section of link id 24027: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24027: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/epi2me-labs\/pychopper\" id=\"link-25702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pychopper<\/a>\n<!-- Time to render name section of link id 25702: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.<\/p>\n<!-- Time to render link large description section of link id 25702: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pychopper> How to use <\/a>\n<!-- Time to render notes section of link id 25702: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25702: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/a-slide\/pycoQC\" id=\"link-24034\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pycoQC<\/a>\n<!-- Time to render name section of link id 24034: 2.1457672119141E-6 --> \n<\/td>\n<td><p>pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore\/Guppy)<\/p>\n<!-- Time to render link large description section of link id 24034: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pycoQC> How to use <\/a>\n<!-- Time to render notes section of link id 24034: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24034: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/genotoul-bioinfo\/pyrocleaner\" id=\"link-24471\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PyroCleaner<\/a>\n<!-- Time to render name section of link id 24471: 3.0994415283203E-6 --> \n<\/td>\n<td><p>PyroCleaner is intended to clean reads coming from pyrosequencing in order to ease the assembly process.<\/p>\n<!-- Time to render link large description section of link id 24471: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24471: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24471: 0.00012016296386719 --> \n<tr><td><a href=\"http:\/\/qualimap.bioinfo.cipf.es\/\" id=\"link-23705\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Qualimap<\/a>\n<!-- Time to render name section of link id 23705: 2.1457672119141E-6 --> \n<\/td>\n<td><p><b>Qualimap 2<\/b> is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.<\/p>\n<!-- Time to render link large description section of link id 23705: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Qualimap> How to use <\/a>\n<!-- Time to render notes section of link id 23705: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23705: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/gmarcais\/Quorum\" id=\"link-24042\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Quorum<\/a>\n<!-- Time to render name section of link id 24042: 1.9073486328125E-6 --> \n<\/td>\n<td><p>QuorUM (Quality Optimized Reads from the University of Maryland) is an error corrector for Illumina reads.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24042: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24042: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24042: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/GuntherLab\/READv2\" id=\"link-25546\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">READv2<\/a>\n<!-- Time to render name section of link id 25546: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Relationship Estimation from Ancient DNA version 2.<\/p>\n<!-- Time to render link large description section of link id 25546: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_READv2> How to use <\/a>\n<!-- Time to render notes section of link id 25546: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25546: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/khyox\/recentrifuge\" id=\"link-25784\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Recentrifuge<\/a>\n<!-- Time to render name section of link id 25784: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Robust comparative analysis and contamination removal for metagenomics<\/p>\n<!-- Time to render link large description section of link id 25784: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Recentrifuge> How to use <\/a>\n<!-- Time to render notes section of link id 25784: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25784: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/rseqc.sourceforge.net\/\" id=\"link-23720\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RSeQC<\/a>\n<!-- Time to render name section of link id 23720: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data<\/p>\n<!-- Time to render link large description section of link id 23720: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RSeQC> How to use <\/a>\n<!-- Time to render notes section of link id 23720: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23720: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/najoshi\/sabre\" id=\"link-23835\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sabre<\/a>\n<!-- Time to render name section of link id 23835: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A barcode demultiplexing and trimming tool for FastQ files.<\/p>\n<!-- Time to render link large description section of link id 23835: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23835: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23835: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/GregoryFaust\/samblaster\" id=\"link-23829\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samblaster<\/a>\n<!-- Time to render name section of link id 23829: 2.1457672119141E-6 --> \n<\/td>\n<td><p>samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and\/or split read mappings to separate SAM files, and\/or unmapped\/clipped reads to a separate FASTQ file.<\/p>\n<!-- Time to render link large description section of link id 23829: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_samblaster> How to use <\/a>\n<!-- Time to render notes section of link id 23829: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23829: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/schmutzi\" id=\"link-23927\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">schmutzi<\/a>\n<!-- Time to render name section of link id 23927: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bayesian maximum a posteriori contamination estimate for ancient samples.<\/p>\n<!-- Time to render link large description section of link id 23927: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_schmutzi> How to use <\/a>\n<!-- Time to render notes section of link id 23927: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23927: 0.00010585784912109 --> \n<tr><td><a href=\"ftp:\/\/occams.dfci.harvard.edu\/pub\/bio\/tgi\/software\/seqclean\/\" id=\"link-23896\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqclean<\/a>\n<!-- Time to render name section of link id 23896: 2.8610229492188E-6 --> \n<\/td>\n<td><p>SeqClean is a tool for validation and trimming of DNA sequences from a flat file database (FASTA format).<\/p>\n<!-- Time to render link large description section of link id 23896: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqclean> How to use <\/a>\n<!-- Time to render notes section of link id 23896: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23896: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/pypi.org\/project\/seqconverter\" id=\"link-26169\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqconverter<\/a>\n<!-- Time to render name section of link id 26169: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The command-line program seqconverter can read and write text files containing aligned or unaligned DNA or protein sequences.<\/p>\n<!-- Time to render link large description section of link id 26169: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqconverter> How to use <\/a>\n<!-- Time to render notes section of link id 26169: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26169: 0.00021600723266602 --> \n<tr><td><a href=\"https:\/\/github.com\/guertinlab\/Tn5bias\" id=\"link-26135\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqOutATACBias<\/a>\n<!-- Time to render name section of link id 26135: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A CLI that corrects the sequence bias of Tn5 transposase in ATAC-seq data using a rule ensemble model.<\/p>\n<!-- Time to render link large description section of link id 26135: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqOutATACBias> How to use <\/a>\n<!-- Time to render notes section of link id 26135: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26135: 0.00012612342834473 --> \n<tr><td><a href=\"https:\/\/guertinlab.github.io\/seqOutBias\/\" id=\"link-26133\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqOutBias<\/a>\n<!-- Time to render name section of link id 26133: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Universal correction of enzymatic sequence bias.<\/p>\n<!-- Time to render link large description section of link id 26133: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqOutBias> How to use <\/a>\n<!-- Time to render notes section of link id 26133: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26133: 0.00019383430480957 --> \n<tr><td><a href=\"https:\/\/github.com\/raymondkiu\/sequence-stats\" id=\"link-25248\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sequence-stats<\/a>\n<!-- Time to render name section of link id 25248: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast and beginner-friendly program to generate statistics from FASTQ and FASTA files (written AWK and Bash), e.g. genome assembly sizes and GC content (%).<\/p>\n<!-- Time to render link large description section of link id 25248: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sequence-stats> How to use <\/a>\n<!-- Time to render notes section of link id 25248: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25248: 0.00017285346984863 --> \n<tr><td><a href=\"https:\/\/github.com\/najoshi\/sickle\" id=\"link-23728\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sickle<\/a>\n<!-- Time to render name section of link id 23728: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.<\/p>\n<!-- Time to render link large description section of link id 23728: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_sickle> How to use <\/a>\n<!-- Time to render notes section of link id 23728: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23728: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/www.pacb.com\/support\/software-downloads\/\" id=\"link-23904\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SMRTLink<\/a>\n<!-- Time to render name section of link id 23904: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SMRT Link is the web-based end-to-end workflow manager for the Sequel\u2122 System. (installed in mode command line on our cluster)<\/p>\n<!-- Time to render link large description section of link id 23904: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SMRTLink> How to use <\/a>\n<!-- Time to render notes section of link id 23904: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23904: 0.00012993812561035 --> \n<tr><td><a href=\"http:\/\/www.bioinf.uni-leipzig.de\/Software\/snoReport\/\" id=\"link-23731\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SnoReport<\/a>\n<!-- Time to render name section of link id 23731: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Computational identification of snoRNAs with unknown targets.<br \/>\r\nDetecting novel or orphan snoRNAs in RNA sequence data using sequence and structure information only without relying on target information<\/p>\n<!-- Time to render link large description section of link id 23731: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23731: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23731: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/calkan\/sonic\" id=\"link-24853\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">sonic<\/a>\n<!-- Time to render name section of link id 24853: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Some Organism's Nucleotide Information Container.<\/p>\n<!-- Time to render link large description section of link id 24853: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24853: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24853: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sprai-doc.readthedocs.io\/en\/latest\/\" id=\"link-24535\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sprai<\/a>\n<!-- Time to render name section of link id 24535: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Sprai (single-pass read accuracy improver) is a tool to correct sequencing errors in single-pass reads for de novo assembly.<\/p>\n<!-- Time to render link large description section of link id 24535: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24535: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24535: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/github.com\/marekborowiec\/spruceup\" id=\"link-24536\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spruceup<\/a>\n<!-- Time to render name section of link id 24536: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tools to discover, visualize, and remove outlier sequences in large multiple sequence alignments.<\/p>\n<!-- Time to render link large description section of link id 24536: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24536: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24536: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/hibberdlab.com\/transrate\/index.html\" id=\"link-23775\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Transrate<\/a>\n<!-- Time to render name section of link id 23775: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Transrate is software for de-novo transcriptome assembly quality analysis.<\/p>\n<!-- Time to render link large description section of link id 23775: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Transrate> How to use <\/a>\n<!-- Time to render notes section of link id 23775: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23775: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/\" id=\"link-23752\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trim Galore<\/a>\n<!-- Time to render name section of link id 23752: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.<\/p>\n<!-- Time to render link large description section of link id 23752: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TrimGalore> How to use <\/a>\n<!-- Time to render notes section of link id 23752: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23752: 0.00011587142944336 --> \n<tr><td><a href=\"http:\/\/www.usadellab.org\/cms\/?page=trimmomatic%20\" id=\"link-23754\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Trimmomatic<\/a>\n<!-- Time to render name section of link id 23754: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.<\/p>\n<!-- Time to render link large description section of link id 23754: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Trimmomatic> How to use <\/a>\n<!-- Time to render notes section of link id 23754: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23754: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/CGATOxford\/UMI-tools\" id=\"link-24092\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">UMI-tools<\/a>\n<!-- Time to render name section of link id 24092: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tools for handling Unique Molecular Identifiers in NGS data sets<\/p>\n<!-- Time to render link large description section of link id 24092: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_UMI-tools> How to use <\/a>\n<!-- Time to render notes section of link id 24092: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24092: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/CobiontID\/unique-kmer-counts\" id=\"link-25441\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">unique-kmer-counts<\/a>\n<!-- Time to render name section of link id 25441: 1.9073486328125E-6 --> \n<\/td>\n<td><p>This program calculates the number of distinct k-mers for each sequence record in a fasta file and divides it by the total number of k-mers in that record.<\/p>\n<!-- Time to render link large description section of link id 25441: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_unique-kmer-counts> How to use <\/a>\n<!-- Time to render notes section of link id 25441: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25441: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/biopet\/vcfstats\" id=\"link-26194\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vcfstats<\/a>\n<!-- Time to render name section of link id 26194: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Vcfstats is a tool that can generate metrics from a vcf file.<\/p>\n<!-- Time to render link large description section of link id 26194: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vcfstats> How to use <\/a>\n<!-- Time to render notes section of link id 26194: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26194: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/HaploKit\/vechat\" id=\"link-24910\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VeChat<\/a>\n<!-- Time to render name section of link id 24910: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Correcting errors in noisy long reads using variation graphs.<\/p>\n<!-- Time to render link large description section of link id 24910: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VeChat> How to use <\/a>\n<!-- Time to render notes section of link id 24910: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24910: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/jjuhyunkim\/verkko-fillet\" id=\"link-26115\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">verkko-fillet<\/a>\n<!-- Time to render name section of link id 26115: 2.1457672119141E-6 --> \n<\/td>\n<td><p>verkko-fillet is an easy-to-use toolkit for cleaning Verkko assemblies.<\/p>\n<!-- Time to render link large description section of link id 26115: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_verkko-fillet> How to use <\/a>\n<!-- Time to render notes section of link id 26115: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26115: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/github.com\/Matthijnssenslab\/ViPER\" id=\"link-25686\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ViPER<\/a>\n<!-- Time to render name section of link id 25686: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bioinformatics pipeline used in the Laboratory of Viral Metagenomics (KU Leuven) to trim and assemble paired-end Illumina reads, and classify resulting contigs.<\/p>\n<!-- Time to render link large description section of link id 25686: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ViPER> How to use <\/a>\n<!-- Time to render notes section of link id 25686: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25686: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/natir\/yacrd\" id=\"link-24100\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">yacrd<\/a>\n<!-- Time to render name section of link id 24100: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Yet Another Chimeric Read Detector for long reads<\/p>\n<!-- Time to render link large description section of link id 24100: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24100: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24100: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/yak\" id=\"link-24598\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Yak<\/a>\n<!-- Time to render name section of link id 24598: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Yak is initially developed for two specific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads.<\/p>\n<!-- Time to render link large description section of link id 24598: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24598: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24598: 9.7990036010742E-5 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    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nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1132 level0\"><!-- Div Category --><div id=\"rad-seq-analysis\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">RAD-seq analysis<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/stevemussmann\/BayesAss3-SNPs\" id=\"link-24155\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayesAss3-SNPs<\/a>\n<!-- Time to render name section of link id 24155: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Modification of BayesAss 3.0.4 to allow handling of large SNP datasets.<\/p>\n<!-- Time to render link large description section of link id 24155: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BayesAss3-SNPs> How to use <\/a>\n<!-- Time to render notes section of link id 24155: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24155: 0.00012016296386719 --> \n<tr><td><a href=\"https:\/\/github.com\/millanek\/fineRADstructure\" id=\"link-24235\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fineRADstructure<\/a>\n<!-- Time to render name section of link id 24235: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A complete, easy to use, and fast population inference package for RAD-seq data.<\/p>\n<!-- Time to render link large description section of link id 24235: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24235: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24235: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/tkchafin\/fragmatic\" id=\"link-24239\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fragmatic<\/a>\n<!-- Time to render name section of link id 24239: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Simple program for in silico restriction digest of genomic sequences, to simulate RAD-family NGS library prep methods.<\/p>\n<!-- Time to render link large description section of link id 24239: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24239: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24239: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/ipyrad.readthedocs.io\/\" id=\"link-23862\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ipyrad<\/a>\n<!-- Time to render name section of link id 23862: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.<\/p>\n<!-- Time to render link large description section of link id 23862: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ipyrad> How to use <\/a>\n<!-- Time to render notes section of link id 23862: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23862: 0.00011014938354492 --> \n<tr><td><a href=\"http:\/\/www1.montpellier.inra.fr\/CBGP\/software\/RADIS\/index.html\" id=\"link-23847\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RADIS<\/a>\n<!-- Time to render name section of link id 23847: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Analysis of RAD-seq data for InterSpecific phylogeny<\/p>\n<!-- Time to render link large description section of link id 23847: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23847: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23847: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/SexGenomicsToolkit\/radsex\" id=\"link-25704\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">radsex<\/a>\n<!-- Time to render name section of link id 25704: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Find sex signal in RAD-Sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25704: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_radsex> How to use <\/a>\n<!-- Time to render notes section of link id 25704: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25704: 0.00011110305786133 --> \n<tr><td><a href=\"http:\/\/catchenlab.life.illinois.edu\/stacks\/\" id=\"link-23739\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Stacks<\/a>\n<!-- Time to render name section of link id 23739: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Stacks is a software suite for analysing RAD Sequencing data by Julian Catchen at the University of Oregon. 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\n                    [post_name] => censor\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 08:07:47\n                    [post_modified_gmt] => 2025-05-21 06:07:47\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/censor\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 25684\n                    [post_author] => 5\n                    [post_date] => 2025-02-26 09:23:53\n                    [post_date_gmt] => 2025-02-26 08:23:53\n                    [post_content] => \n                    [post_title] => centroAnno\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => centroanno\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-03-02 20:07:55\n                    [post_modified_gmt] => 2025-03-02 19:07:55\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25684\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 25314\n                    [post_author] => 5\n                    [post_date] => 2024-03-18 10:35:49\n                    [post_date_gmt] => 2024-03-18 09:35:49\n                    [post_content] => \n                    [post_title] => cnD\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => cnd\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-28 14:03:57\n                    [post_modified_gmt] => 2024-03-28 13:03:57\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25314\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 25335\n                    [post_author] => 5\n                    [post_date] => 2024-04-02 08:57:27\n                    [post_date_gmt] => 2024-04-02 06:57:27\n                    [post_content] => \n                    [post_title] => EarlGrey\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => earlgrey\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-17 08:51:31\n                    [post_modified_gmt] => 2024-06-17 06:51:31\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25335\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [4] => WP_Post Object\n                (\n                    [ID] => 26147\n                    [post_author] => 5\n                    [post_date] => 2025-11-20 10:55:25\n                    [post_date_gmt] => 2025-11-20 09:55:25\n                    [post_content] => \n                    [post_title] => ExpansionHunter\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => expansionhunter\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-01-03 11:29:57\n                    [post_modified_gmt] => 2026-01-03 10:29:57\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26147\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [5] => WP_Post Object\n                (\n                    [ID] => 25334\n                    [post_author] => 5\n                    [post_date] => 2024-04-02 08:44:44\n                    [post_date_gmt] => 2024-04-02 06:44:44\n                    [post_content] => \n                    [post_title] => GraffiTE\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => graffite\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-19 09:48:25\n                    [post_modified_gmt] => 2024-06-19 07:48:25\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25334\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [6] => WP_Post Object\n                (\n                    [ID] => 26144\n                    [post_author] => 5\n                    [post_date] => 2025-11-18 07:23:32\n                    [post_date_gmt] => 2025-11-18 06:23:32\n                    [post_content] => \n                    [post_title] => HipSTR\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => hipstr\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2026-01-03 11:38:08\n                    [post_modified_gmt] => 2026-01-03 10:38:08\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26144\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [7] => WP_Post Object\n                (\n                    [ID] => 25280\n                    [post_author] => 5\n                    [post_date] => 2024-03-06 09:43:14\n                    [post_date_gmt] => 2024-03-06 08:43:14\n                    [post_content] => \n                    [post_title] => ICEscreen\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => icescreen\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-12 10:20:23\n                    [post_modified_gmt] => 2024-03-12 09:20:23\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25280\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [8] => WP_Post Object\n                (\n                    [ID] => 26177\n                    [post_author] => 5\n                    [post_date] => 2025-12-17 16:47:26\n                    [post_date_gmt] => 2025-12-17 15:47:26\n                    [post_content] => \n                    [post_title] => ISEScan\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => isescan\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-12-30 16:26:16\n                    [post_modified_gmt] => 2025-12-30 15:26:16\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=26177\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [9] => WP_Post Object\n                (\n                    [ID] => 25164\n                    [post_author] => 5\n                    [post_date] => 2023-12-19 15:32:18\n                    [post_date_gmt] => 2023-12-19 14:32:18\n                    [post_content] => \n                    [post_title] => Look4TRs\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => look4trs\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-02-28 10:25:36\n                    [post_modified_gmt] => 2024-02-28 09:25:36\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25164\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [10] => WP_Post Object\n                (\n                    [ID] => 24359\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:55\n                    [post_date_gmt] => 2022-11-22 09:25:55\n                    [post_content] => \n                    [post_title] => LTR_FINDER_parallel\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => ltr_finder_parallel\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-07-29 08:09:12\n                    [post_modified_gmt] => 2025-07-29 06:09:12\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/ltr_finder_parallel\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 24360\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:53\n                    [post_date_gmt] => 2022-11-22 09:25:53\n                    [post_content] => \n                    [post_title] => LtrDetector\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => ltrdetector\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:17:25\n                    [post_modified_gmt] => 2025-05-22 07:17:25\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/ltrdetector\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [12] => WP_Post Object\n                (\n                    [ID] => 25758\n                    [post_author] => 5\n                    [post_date] => 2025-04-08 10:15:28\n                    [post_date_gmt] => 2025-04-08 08:15:28\n                    [post_content] => \n                    [post_title] => MCHelper\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => mchelper\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-06-25 11:31:16\n                    [post_modified_gmt] => 2025-06-25 09:31:16\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25758\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [13] => WP_Post Object\n                (\n                    [ID] => 23666\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 12:19:19\n                    [post_date_gmt] => 2022-11-22 11:19:19\n                    [post_content] => \n                    [post_title] => MinCED\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => minced\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:41:03\n                    [post_modified_gmt] => 2025-05-22 07:41:03\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/minced\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [14] => WP_Post Object\n                (\n                    [ID] => 23669\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 12:19:19\n                    [post_date_gmt] => 2022-11-22 11:19:19\n                    [post_content] => \n                    [post_title] => Mobster\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => mobster\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:43:54\n                    [post_modified_gmt] => 2025-05-22 07:43:54\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/mobster\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [15] => WP_Post Object\n                (\n                    [ID] => 24398\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:05\n                    [post_date_gmt] => 2022-11-22 09:26:05\n                    [post_content] => \n                    [post_title] => mreps\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => mreps\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:45:44\n                    [post_modified_gmt] => 2025-05-22 07:45:44\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/mreps\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [16] => WP_Post Object\n                (\n                    [ID] => 25252\n                    [post_author] => 5\n                    [post_date] => 2024-02-14 09:31:10\n                    [post_date_gmt] => 2024-02-14 08:31:10\n                    [post_content] => \n                    [post_title] => MSIsensor-pro\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => msisensor-pro\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-12 10:24:11\n                    [post_modified_gmt] => 2024-03-12 09:24:11\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25252\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [17] => WP_Post Object\n                (\n                    [ID] => 23923\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 12:19:34\n                    [post_date_gmt] => 2022-11-22 11:19:34\n                    [post_content] => \n                    [post_title] => NSEG\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => nseg\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 09:59:00\n                    [post_modified_gmt] => 2025-05-22 07:59:00\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/nseg\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [18] => WP_Post Object\n                (\n                    [ID] => 24422\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:54\n                    [post_date_gmt] => 2022-11-22 09:25:54\n                    [post_content] => \n                    [post_title] => ntHits\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => nthits\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 10:00:04\n                    [post_modified_gmt] => 2025-05-22 08:00:04\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/nthits\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [19] => WP_Post Object\n                (\n                    [ID] => 24426\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:07\n                    [post_date_gmt] => 2022-11-22 09:26:07\n                    [post_content] => \n                    [post_title] => Onecodetofindthemall\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => onecodetofindthemall\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-22 14:12:10\n                    [post_modified_gmt] => 2025-05-22 12:12:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/onecodetofindthemall\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [20] => WP_Post Object\n                (\n                    [ID] => 26096\n                    [post_author] => 5\n                    [post_date] => 2025-09-15 11:24:21\n                    [post_date_gmt] => 2025-09-15 09:24:21\n                    [post_content] => \n                    [post_title] => pantera\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => pantera\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-12-30 15:54:12\n                    [post_modified_gmt] => 2025-12-30 14:54:12\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => 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class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"http:\/\/www.girinst.org\/downloads\/software\/censor\/\" id=\"link-23853\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CENSOR<\/a>\n<!-- Time to render name section of link id 23853: 6.9141387939453E-6 --> \n<\/td>\n<td><p>CENSOR compares and masks protein or nucleotide sequences.<\/p>\n<!-- Time to render link large description section of link id 23853: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CENSOR> How to use <\/a>\n<!-- Time to render notes section of link id 23853: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23853: 0.00035810470581055 --> \n<tr><td><a href=\"https:\/\/github.com\/junhaiqi\/centroAnno\" id=\"link-25684\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">centroAnno<\/a>\n<!-- Time to render name section of link id 25684: 6.9141387939453E-6 --> \n<\/td>\n<td><p>centroAnno is a prior-independent tool for automatic and efficient centromere\/tendem repeat structural analysis across multiple species. centroAnno supports the analysis of repeat units and higher-order tandem repeat units (HORs) in genome\/assembly, centromere sequence, and single sequencing long read.<\/p>\n<!-- Time to render link large description section of link id 25684: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_centroAnno> How to use <\/a>\n<!-- Time to render notes section of link id 25684: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25684: 0.00033903121948242 --> \n<tr><td><a href=\"https:\/\/ftp.sanger.ac.uk\/pub\/resources\/software\/cnd\/\" id=\"link-25314\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cnD<\/a>\n<!-- Time to render name section of link id 25314: 7.1525573730469E-6 --> \n<\/td>\n<td><p>cnD is a program to detect copy number variants from short-read sequence data.<\/p>\n<!-- Time to render link large description section of link id 25314: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cnD> How to use <\/a>\n<!-- Time to render notes section of link id 25314: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25314: 0.0003359317779541 --> \n<tr><td><a href=\"https:\/\/github.com\/TobyBaril\/EarlGrey\" id=\"link-25335\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EarlGrey<\/a>\n<!-- Time to render name section of link id 25335: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A fully automated TE curation and annotation pipeline.<\/p>\n<!-- Time to render link large description section of link id 25335: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EarlGrey> How to use <\/a>\n<!-- Time to render notes section of link id 25335: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25335: 0.00033211708068848 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/ExpansionHunter\" id=\"link-26147\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ExpansionHunter<\/a>\n<!-- Time to render name section of link id 26147: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A tool for estimating repeat sizes.<\/p>\n<!-- Time to render link large description section of link id 26147: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ExpansionHunter> How to use <\/a>\n<!-- Time to render notes section of link id 26147: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26147: 0.0002129077911377 --> \n<tr><td><a href=\"https:\/\/github.com\/cgroza\/GraffiTE\" id=\"link-25334\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraffiTE<\/a>\n<!-- Time to render name section of link id 25334: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and\/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.<\/p>\n<!-- Time to render link large description section of link id 25334: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GraffiTE> How to use <\/a>\n<!-- Time to render notes section of link id 25334: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25334: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/HipSTR-Tool\/HipSTR\" id=\"link-26144\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HipSTR<\/a>\n<!-- Time to render name section of link id 26144: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Genotype and phase short tandem repeats using Illumina whole-genome sequencing data.<\/p>\n<!-- Time to render link large description section of link id 26144: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HipSTR> How to use <\/a>\n<!-- Time to render notes section of link id 26144: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26144: 0.00019598007202148 --> \n<tr><td><a href=\"https:\/\/icescreen.migale.inrae.fr\" id=\"link-25280\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ICEscreen<\/a>\n<!-- Time to render name section of link id 25280: 4.0531158447266E-6 --> \n<\/td>\n<td><p>ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes.<\/p>\n<!-- Time to render link large description section of link id 25280: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ICEscreen> How to use <\/a>\n<!-- Time to render notes section of link id 25280: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25280: 0.00016617774963379 --> \n<tr><td><a href=\"https:\/\/github.com\/xiezhq\/ISEScan\" id=\"link-26177\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ISEScan<\/a>\n<!-- Time to render name section of link id 26177: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome.<\/p>\r\n<p>ISEScan can be used to identify\/annotate full-length or non-full-length IS elements in any DNA sequence but ISEScan was only tested on prokarytoic genome including draft genome and meta-genome.<\/p>\r\n<p>Among the existing tools identifying IS elements, ISEScan might be the only one that gives TIR (Terminal Inverted Repeat) sequences.<\/p>\n<!-- Time to render link large description section of link id 26177: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ISEScan> How to use <\/a>\n<!-- Time to render notes section of link id 26177: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26177: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/BioinformaticsToolsmith\/Look4TRs\" id=\"link-25164\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Look4TRs<\/a>\n<!-- Time to render name section of link id 25164: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A de-novo tool for detecting simple tandem repeats using self-supervised hidden Markov models.<\/p>\n<!-- Time to render link large description section of link id 25164: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Look4TRs> How to use <\/a>\n<!-- Time to render notes section of link id 25164: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25164: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/oushujun\/LTR_FINDER_parallel\" id=\"link-24359\" class=\"track_this_link \" rel=\"noopener noreferrer\">LTR_FINDER_parallel<\/a>\n<!-- Time to render name section of link id 24359: 3.814697265625E-6 --> \n<\/td>\n<td><p>A parallel wrapper for LTR_FINDER (LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.)<\/p>\n<!-- Time to render link large description section of link id 24359: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24359: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24359: 0.00016307830810547 --> \n<tr><td><a href=\"https:\/\/github.com\/TulsaBioinformaticsToolsmith\/LtrDetector\" id=\"link-24360\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LtrDetector<\/a>\n<!-- Time to render name section of link id 24360: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A tool-suite for detecting long terminal repeat retrotransposons de-novo on the genomic scale.<\/p>\n<!-- Time to render link large description section of link id 24360: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LtrDetector> How to use <\/a>\n<!-- Time to render notes section of link id 24360: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24360: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/GonzalezLab\/MCHelper\" id=\"link-25758\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MCHelper<\/a>\n<!-- Time to render name section of link id 25758: 3.0994415283203E-6 --> \n<\/td>\n<td><p>An automatic tool to curate transposable element libraries.<\/p>\n<!-- Time to render link large description section of link id 25758: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MCHelper> How to use <\/a>\n<!-- Time to render notes section of link id 25758: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25758: 0.00016188621520996 --> \n<tr><td><a href=\"https:\/\/github.com\/ctSkennerton\/minced\/\" id=\"link-23666\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MinCED<\/a>\n<!-- Time to render name section of link id 23666: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the command-line and was derived from CRT<\/p>\n<!-- Time to render link large description section of link id 23666: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23666: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23666: 0.00015711784362793 --> \n<tr><td><a href=\"https:\/\/github.com\/jyhehir\/mobster\" id=\"link-23669\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mobster<\/a>\n<!-- Time to render name section of link id 23669: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Mobster is used to detect novel (non-reference) Mobile Element Insertion (MEI) events in BAM files and uses both a discordant read pair method and a split-read method.<\/p>\n<!-- Time to render link large description section of link id 23669: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23669: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23669: 0.00015997886657715 --> \n<tr><td><a href=\"http:\/\/mreps.univ-mlv.fr\" id=\"link-24398\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mreps<\/a>\n<!-- Time to render name section of link id 24398: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Software for tandem repeat identification in DNA.<\/p>\n<!-- Time to render link large description section of link id 24398: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mreps> How to use <\/a>\n<!-- Time to render notes section of link id 24398: 2.1457672119141E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24398: 0.00016903877258301 --> \n<tr><td><a href=\"https:\/\/github.com\/xjtu-omics\/msisensor-pro\" id=\"link-25252\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MSIsensor-pro<\/a>\n<!-- Time to render name section of link id 25252: 3.0994415283203E-6 --> \n<\/td>\n<td><p>MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25252: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MSIsensor-pro> How to use <\/a>\n<!-- Time to render notes section of link id 25252: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25252: 0.00016999244689941 --> \n<tr><td><a href=\"ftp:\/\/ftp.ncbi.nih.gov\/pub\/seg\/nseg\/\" id=\"link-23923\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NSEG<\/a>\n<!-- Time to render name section of link id 23923: 2.8610229492188E-6 --> \n<\/td>\n<td><p>NSEG is used to mask nucleic acid sequences, needed by RepeatScout.<\/p>\n<!-- Time to render link large description section of link id 23923: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NSEG> How to use <\/a>\n<!-- Time to render notes section of link id 23923: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23923: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/bcgsc\/ntHits\" id=\"link-24422\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ntHits<\/a>\n<!-- Time to render name section of link id 24422: 3.0994415283203E-6 --> \n<\/td>\n<td><p>ntHits is a method for identifying reapeats in high-throughput DNA sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24422: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24422: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24422: 0.00016999244689941 --> \n<tr><td><a href=\"http:\/\/doua.prabi.fr\/software\/one-code-to-find-them-all\" id=\"link-24426\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Onecodetofindthemall<\/a>\n<!-- Time to render name section of link id 24426: 3.0994415283203E-6 --> \n<\/td>\n<td><p>One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information.<\/p>\n<!-- Time to render link large description section of link id 24426: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24426: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24426: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/piosierra\/pantera\" id=\"link-26096\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pantera<\/a>\n<!-- Time to render name section of link id 26096: 3.0994415283203E-6 --> \n<\/td>\n<td><p class=\"heading-element\" dir=\"auto\">Identification of transposable element families from pangenome polymorphisms. A pangenome is a collection of genomes or haplotypes that can be aligned and stored as a variation graph in gfa format. pantera receives as input a list of gfa files of non overlapping variation graphs and produces a library of transposable elements found to be polymorphic on that pangenome.<\/p>\n<!-- Time to render link large description section of link id 26096: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pantera> How to use <\/a>\n<!-- Time to render notes section of link id 26096: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26096: 0.0001838207244873 --> \n<tr><td><a href=\"https:\/\/github.com\/4ureliek\/Parsing-RepeatMasker-Outputs\" id=\"link-24433\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">parseRM<\/a>\n<!-- Time to render name section of link id 24433: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Few scripts facilitating the extraction of info from Repeat Masker .out files<\/p>\n<!-- Time to render link large description section of link id 24433: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24433: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24433: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/www.drive5.com\/piler\/\" id=\"link-24446\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PILER<\/a>\n<!-- Time to render name section of link id 24446: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Genomic repeat analysis software.<\/p>\n<!-- Time to render link large description section of link id 24446: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PILER> How to use <\/a>\n<!-- Time to render notes section of link id 24446: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24446: 0.00016689300537109 --> \n<tr><td><a href=\"http:\/\/www.drive5.com\/pilercr\/\" id=\"link-24447\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PILERCR<\/a>\n<!-- Time to render name section of link id 24447: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PILERCR is public domain software for finding CRISPR repeats.<\/p>\n<!-- Time to render link large description section of link id 24447: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24447: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24447: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/rdxplorer.sourceforge.net\/\" id=\"link-25313\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDXplorer<\/a>\n<!-- Time to render name section of link id 25313: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The RDXplorer (Read Depth eXplorer) is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.<\/p>\n<!-- Time to render link large description section of link id 25313: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RDXplorer> How to use <\/a>\n<!-- Time to render notes section of link id 25313: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25313: 0.00016999244689941 --> \n<tr><td><a href=\"http:\/\/eddylab.org\/software\/recon\/\" id=\"link-23924\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RECON<\/a>\n<!-- Time to render name section of link id 23924: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A package for automated de novo identification of repeat families from genomic sequence.<\/p>\n<!-- Time to render link large description section of link id 23924: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RECON> How to use <\/a>\n<!-- Time to render notes section of link id 23924: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23924: 0.00015997886657715 --> \n<tr><td><a href=\"https:\/\/github.com\/bioinfomaticsCSU\/RepAHR\" id=\"link-24490\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepAHR<\/a>\n<!-- Time to render name section of link id 24490: 3.0994415283203E-6 --> \n<\/td>\n<td><p>RepAHR is used to identify repeats(repetitive sequences) in genome using Next-Generation Sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24490: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24490: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24490: 0.00015902519226074 --> \n<tr><td><a href=\"https:\/\/github.com\/simoncchu\/REPdenovo\" id=\"link-24491\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REPdenovo<\/a>\n<!-- Time to render name section of link id 24491: 3.0994415283203E-6 --> \n<\/td>\n<td><p>REPdenovo is designed for constructing repeats directly from sequence (paired-end) reads. It based on the idea of frequent k-mer assembly. REPdenovo provides many functionalities, and can generate much longer repeats than existing tools. Internally, REPdenovo uses Jellyfish for k-mer counting, Velvet for assembly, and bwa to map reads on the Transposable Elements.<\/p>\n<!-- Time to render link large description section of link id 24491: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24491: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24491: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/github.com\/Dfam-consortium\/RepeatAfterMe\" id=\"link-26131\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatAfterMe<\/a>\n<!-- Time to render name section of link id 26131: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A package for the extension of repetitive DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 26131: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RepeatAfterMe> How to use <\/a>\n<!-- Time to render notes section of link id 26131: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26131: 0.00016498565673828 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/petrnovak\/repex_tarean\/src\/devel\/\" id=\"link-24492\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatExplorer<\/a>\n<!-- Time to render name section of link id 24492: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes.<\/p>\n<!-- Time to render link large description section of link id 24492: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24492: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24492: 0.00010490417480469 --> \n<tr><td><a href=\"http:\/\/www.repeatmasker.org\/\" id=\"link-23714\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatMasker<\/a>\n<!-- Time to render name section of link id 23714: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RepeatMasker is a program that screens DNA sequences for interspersed repeats (thanks to RepBase repeats databanks specially formatted) and low complexity DNA sequences.<\/p>\n<!-- Time to render link large description section of link id 23714: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RepeatMasker> How to use <\/a>\n<!-- Time to render notes section of link id 23714: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23714: 9.9897384643555E-5 --> \n<tr><td><a href=\"http:\/\/www.repeatmasker.org\/RepeatModeler.html\" id=\"link-23715\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatModeler<\/a>\n<!-- Time to render name section of link id 23715: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RepeatModeler is a de-novo repeat family identification and modeling package.<\/p>\n<!-- Time to render link large description section of link id 23715: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RepeatModeler> How to use <\/a>\n<!-- Time to render notes section of link id 23715: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23715: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/Dfam-consortium\/RepeatScout\" id=\"link-23716\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepeatScout<\/a>\n<!-- Time to render name section of link id 23716: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RepeatScout is a tool to discover repetitive substrings in DNA.<\/p>\n<!-- Time to render link large description section of link id 23716: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RepeatScout> How to use <\/a>\n<!-- Time to render notes section of link id 23716: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23716: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/nerettilab\/RepEnrich2\" id=\"link-24024\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RepEnrich2<\/a>\n<!-- Time to render name section of link id 24024: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24024: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24024: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24024: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/urgi.versailles.inra.fr\/Tools\/REPET\" id=\"link-23717\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REPET<\/a>\n<!-- Time to render name section of link id 23717: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The<b>\u00a0REPET <\/b><b>package<\/b> (t Flutre <i>et al<\/i>, 2011 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale.<\/p>\n<!-- Time to render link large description section of link id 23717: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REPET> How to use <\/a>\n<!-- Time to render notes section of link id 23717: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23717: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/tk2\/RetroSeq\" id=\"link-24049\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RetroSeq<\/a>\n<!-- Time to render name section of link id 24049: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.<\/p>\n<!-- Time to render link large description section of link id 24049: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24049: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24049: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/REViewer\" id=\"link-25729\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REViewer<\/a>\n<!-- Time to render name section of link id 25729: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool for visualizing alignments of reads in regions containing tandem repeats<\/p>\n<!-- Time to render link large description section of link id 25729: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REViewer> How to use <\/a>\n<!-- Time to render notes section of link id 25729: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25729: 9.7036361694336E-5 --> \n<tr><td><a href=\"http:\/\/www.repeatmasker.org\/RMBlast.html\" id=\"link-23718\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RMBlast<\/a>\n<!-- Time to render name section of link id 23718: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program \"rmblastn\" for use with RepeatMasker and RepeatModeler. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:<br \/>\r\n<br \/>\r\n\u00a0\u00a0 - Support for custom matrices ( without KA-Statistics ).<br \/>\r\n\u00a0\u00a0\u00a0 - Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.<br \/>\r\n\u00a0\u00a0\u00a0 - Support for cross_match-like masklevel filtering.<\/p>\n<!-- Time to render link large description section of link id 23718: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_rmblast-2.13.0> How to use <\/a>\n<!-- Time to render notes section of link id 23718: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23718: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/vpc-ccg\/sedef\" id=\"link-24028\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SEDEF<\/a>\n<!-- Time to render name section of link id 24028: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SEDEF is a quick tool to find all segmental duplications in the genome.<\/p>\n<!-- Time to render link large description section of link id 24028: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24028: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24028: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/HCGB-IGTP\/spaTyper\" id=\"link-24532\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spaTyper<\/a>\n<!-- Time to render name section of link id 24532: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Computational method for finding spa types. Staphylococcus aureus\u00a0is a major human pathogen causing skin and tissue infections, pneumonia, septicemia, and device-associated infections. The emergence of strains resistant to methicillin (MRSA) and other antibacterial agents has become a major concern, especially in the hospital environment, because of the high mortality of the infections caused by these strains. Single locus DNA-sequencing of the repeat region of the\u00a0Staphylococcus\u00a0protein A gene (spa) can be used for reliable, accurate and discriminatory typing of MRSA. Repeats are assigned a numerical code and the spa-type is deduced from the order of specific repeats. However, spa-typing was hampered in the past by the lack of a consensus on assignments of new spa-repeats and -types.<\/p>\n<!-- Time to render link large description section of link id 24532: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24532: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24532: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/wyang17\/SQuIRE\" id=\"link-24539\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SQuIRE<\/a>\n<!-- Time to render name section of link id 24539: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SQuIRE reveals locus-specific regulation of interspersed repeat expression, Nucleic Acids Research<\/p>\n<!-- Time to render link large description section of link id 24539: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SQuIRE> How to use <\/a>\n<!-- Time to render notes section of link id 24539: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24539: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/srf\" id=\"link-26140\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SRF<\/a>\n<!-- Time to render name section of link id 26140: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Satellite Repeat Finder, or SRF in brief, assembles motifs in satellite DNA that are tandemly repeated many times in the genome.<\/p>\n<!-- Time to render link large description section of link id 26140: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SRF> How to use <\/a>\n<!-- Time to render notes section of link id 26140: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26140: 0.00017499923706055 --> \n<tr><td><a href=\"https:\/\/github.com\/GonzalezLab\/T-lex3\" id=\"link-24555\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T-lex<\/a>\n<!-- Time to render name section of link id 24555: 2.1457672119141E-6 --> \n<\/td>\n<td><p>T-lex is a computational pipeline that detects presence and\/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data.<\/p>\n<!-- Time to render link large description section of link id 24555: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24555: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24555: 0.00011491775512695 --> \n<tr><td><a href=\"http:\/\/tandem.bu.edu\/trf\/trf.html\" id=\"link-23747\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tandem Repeats Finder<\/a>\n<!-- Time to render name section of link id 23747: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides.<\/p>\n<!-- Time to render link large description section of link id 23747: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TRF> How to use <\/a>\n<!-- Time to render notes section of link id 23747: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23747: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/urgi-anagen\/te_finder\" id=\"link-25695\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TE_finder<\/a>\n<!-- Time to render name section of link id 25695: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.<\/p>\n<!-- Time to render link large description section of link id 25695: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TE_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25695: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25695: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/zhangrengang\/TEsorter\" id=\"link-24560\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TEsorter<\/a>\n<!-- Time to render name section of link id 24560: 1.9073486328125E-6 --> \n<\/td>\n<td><p>It is coded for LTR_retriever to classify long terminal repeat retrotransposons (LTR-RTs) at first. It can also be used to classify any other TE sequences, including Class I and Class II elements which are covered by the REXdb database.<\/p>\n<!-- Time to render link large description section of link id 24560: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TEsorter> How to use <\/a>\n<!-- Time to render notes section of link id 24560: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24560: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/Dfam-consortium\/TETools\" id=\"link-25666\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TETools<\/a>\n<!-- Time to render name section of link id 25666: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg. This container is an easy way to get a minimal yet fully functional installation of RepeatMasker and RepeatModeler and is additionally useful for testing or reproducibility purposes.<\/p>\n<!-- Time to render link large description section of link id 25666: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TETools> How to use <\/a>\n<!-- Time to render notes section of link id 25666: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25666: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/tolkit\/telomeric-identifier\" id=\"link-24563\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">tidk<\/a>\n<!-- Time to render name section of link id 24563: 2.1457672119141E-6 --> \n<\/td>\n<td><p>tidk is a toolkit to identify and visualise telomeric repeats for the Darwin Tree of Life genomes.<\/p>\n<!-- Time to render link large description section of link id 24563: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_tidk> How to use <\/a>\n<!-- Time to render notes section of link id 24563: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24563: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/danillo-alvarenga\/tn3-ta_finder\" id=\"link-25339\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tn3+TA_finder<\/a>\n<!-- Time to render name section of link id 25339: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tn3 Transposon\/Toxin Finder (Tn3+TA_finder) is a program for the automatic prediction of transposable elements of the Tn3 family associated with type II toxin and antitoxin pairs in bacteria and archaea.<\/p>\n<!-- Time to render link large description section of link id 25339: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Tn3-TA_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25339: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25339: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/danillo-alvarenga\/tncomp_finder\" id=\"link-25338\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TnComp_finder<\/a>\n<!-- Time to render name section of link id 25338: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Composite Transposon Finder (TnComp_finder) is a program for the prediction of putative composite transposons in bacterial and archaeal genomes based on insertion sequence replicas in a relatively short span.<\/p>\n<!-- Time to render link large description section of link id 25338: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TnComp_finder> How to use <\/a>\n<!-- Time to render notes section of link id 25338: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25338: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/DerKevinRiehl\/transposon_annotation_tools\" id=\"link-24570\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">transposon_annotation_tools<\/a>\n<!-- Time to render name section of link id 24570: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of bioconda packages for transposon annotation and transposon feature annotation in nucleotide sequences. transposon_annotation_tools is part of TransposonUltimate. The package includes a series of transposable element discovery tools, such as: MUSTv2, HelitronScanner, SineFinder, MiteTracker, MiteFinderII, SineScan, TirVish, LtrHarvest, RepeatModeler, TransposonPSI, and TransposonProteinNCBICDD1000. You can then use these tools independently.<\/p>\n<!-- Time to render link large description section of link id 24570: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_transposon_annotation_tools> How to use <\/a>\n<!-- Time to render notes section of link id 24570: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24570: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/DerKevinRiehl\/transposon_classifier_rfsb\" id=\"link-25186\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">transposon_classifier_rfsb<\/a>\n<!-- Time to render name section of link id 25186: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Transposon classification tool for nucleotide sequence classification, providing classification, model training and prediction evaluation. <em>RFSB<\/em> is part of <a href=\"https:\/\/github.com\/DerKevinRiehl\/TransposonUltimate\">TransposonUltimate<\/a>.<\/p>\n<!-- Time to render link large description section of link id 25186: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_transposon_classifier_rfsb> How to use <\/a>\n<!-- Time to render notes section of link id 25186: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25186: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/vlothec\/TRASH\" id=\"link-25165\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TRASH<\/a>\n<!-- Time to render name section of link id 25165: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tandem Repeat Annotation and Structural Hierarchy: a package to identify and extract tandem repeats in genome sequences and investigate their higher order structures.<\/p>\n<!-- Time to render link large description section of link id 25165: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TRASH> How to use <\/a>\n<!-- Time 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class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Ribo-seq<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/ohlerlab.mdc-berlin.de\/software\/RiboTaper_126\/\" id=\"link-24041\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RiboTaper<\/a>\n<!-- Time to render name section of link id 24041: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.<\/p>\n<!-- Time to render link large description section of 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[is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => b1e533c3d60b14dcfc84b1a9b6bc5763\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0007178783416748-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1145 level0\"><!-- Div Category --><div id=\"scdna\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">scDNA<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/single-cell-multiome-atac-gex\/software\/overview\/welcome\" id=\"link-24173\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellRanger ARC<\/a>\n<!-- Time to render name section of link id 24173: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cell Ranger ARC's pipelines analyze sequencing data produced from Chromium Single Cell Multiome ATAC + Gene Expression.<\/p>\n<!-- Time to render link large description section of link id 24173: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellRangerARC> How to use <\/a>\n<!-- Time to render notes section of link id 24173: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24173: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/single-cell-genetics\/cellsnp-lite\" id=\"link-25928\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cellsnp-lite<\/a>\n<!-- Time to render name section of link id 25928: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Cellsnp-lite is a C\/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs.<\/p>\n<!-- Time to render link large description section of link id 25928: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cellsnp-lite> How to use <\/a>\n<!-- Time to render notes section of link id 25928: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25928: 0.00010085105895996 --> \n<tr><td><a href=\"https:\/\/github.com\/dpeerlab\/SEACells\" id=\"link-25223\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SEACells<\/a>\n<!-- Time to render name section of link id 25223: 1.9073486328125E-6 --> \n<\/td>\n<td><p dir=\"auto\"><strong>S<\/strong>ingle-c<strong>E<\/strong>ll <strong>A<\/strong>ggregation for High Resolution <strong>Cell S<\/strong>tates.<\/p>\r\n<p class=\"f4 my-3\">SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data.<\/p>\n<!-- Time to render link large description section of link id 25223: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SEACells> How to use <\/a>\n<!-- Time to render notes section of link id 25223: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25223: 0.00010204315185547 --> \n<tr><td><a href=\"https:\/\/github.com\/wheaton5\/souporcell\" id=\"link-25263\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">souporcell<\/a>\n<!-- Time to render name section of link id 25263: 1.9073486328125E-6 --> \n<\/td>\n<td><p>souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.<\/p>\n<!-- Time to render link large description section of link id 25263: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a 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      [field] => term_id\n                        )\n\n                )\n\n            [primary_table] => wp_posts\n            [primary_id_column] => ID\n        )\n\n    [meta_query] => WP_Meta_Query Object\n        (\n            [queries] => Array\n                (\n                )\n\n            [relation] => \n            [meta_table] => \n            [meta_id_column] => \n            [primary_table] => \n            [primary_id_column] => \n            [table_aliases:protected] => Array\n                (\n                )\n\n            [clauses:protected] => Array\n                (\n                )\n\n            [has_or_relation:protected] => \n        )\n\n    [date_query] => \n    [request] => \n\t\t\tSELECT   wp_posts.*\n\t\t\tFROM wp_posts  LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id)\n\t\t\tWHERE 1=1  AND ( \n  wp_term_relationships.term_taxonomy_id IN (1127)\n) AND wp_posts.post_type = 'link_library_links' AND ((wp_posts.post_status = 'publish'))\n\t\t\tGROUP BY wp_posts.ID\n\t\t\tORDER BY wp_posts.post_title ASC\n\t\t\t\n\t\t\n    [posts] => Array\n        (\n            [0] => WP_Post Object\n                (\n                    [ID] => 25351\n                    [post_author] => 5\n                    [post_date] => 2024-04-22 15:06:18\n                    [post_date_gmt] => 2024-04-22 13:06:18\n                    [post_content] => \n                    [post_title] => 3rdChimeraMiner\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => 3rdchimeraminer\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-06-03 09:16:10\n                    [post_modified_gmt] => 2024-06-03 07:16:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25351\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [1] => WP_Post Object\n                (\n                    [ID] => 23939\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:44\n                    [post_date_gmt] => 2022-11-22 09:25:44\n                    [post_content] => \n                    [post_title] => AC-DIAMOND\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => ac-diamond\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:20:48\n                    [post_modified_gmt] => 2025-05-21 05:20:48\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/ac-diamond\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [2] => WP_Post Object\n                (\n                    [ID] => 24133\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:57\n                    [post_date_gmt] => 2022-11-22 09:25:57\n                    [post_content] => \n                    [post_title] => Accel-align\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => accel-align\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:21:08\n                    [post_modified_gmt] => 2025-05-21 05:21:08\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/accel-align\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [3] => WP_Post Object\n                (\n                    [ID] => 25570\n                    [post_author] => 5\n                    [post_date] => 2024-10-28 14:12:20\n                    [post_date_gmt] => 2024-10-28 13:12:20\n                    [post_content] => \n                    [post_title] => ALFATClust\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => alfatclust\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-11-20 11:37:56\n                    [post_modified_gmt] => 2024-11-20 10:37:56\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25570\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [4] => WP_Post Object\n                (\n                    [ID] => 25483\n                    [post_author] => 5\n                    [post_date] => 2024-07-11 13:55:37\n                    [post_date_gmt] => 2024-07-11 11:55:37\n                    [post_content] => \n                    [post_title] => AMBER\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => amber\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-08-12 08:10:09\n                    [post_modified_gmt] => 2024-08-12 06:10:09\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25483\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [5] => WP_Post Object\n                (\n                    [ID] => 24859\n                    [post_author] => 5\n                    [post_date] => 2023-05-25 11:32:44\n                    [post_date_gmt] => 2023-05-25 09:32:44\n                    [post_content] => \n                    [post_title] => AnchorWave\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => anchorwave\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:26:25\n                    [post_modified_gmt] => 2025-05-21 05:26:25\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24859\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [6] => WP_Post Object\n                (\n                    [ID] => 24708\n                    [post_author] => 5\n                    [post_date] => 2023-01-26 11:58:23\n                    [post_date_gmt] => 2023-01-26 10:58:23\n                    [post_content] => \n                    [post_title] => AvP\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => avp\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:32:10\n                    [post_modified_gmt] => 2025-05-21 05:32:10\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=24708\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [7] => WP_Post Object\n                (\n                    [ID] => 25269\n                    [post_author] => 5\n                    [post_date] => 2024-02-29 11:06:34\n                    [post_date_gmt] => 2024-02-29 10:06:34\n                    [post_content] => \n                    [post_title] => Back_to_sequences\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => back_to_sequences\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-03-12 10:12:54\n                    [post_modified_gmt] => 2024-03-12 09:12:54\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25269\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [8] => WP_Post Object\n                (\n                    [ID] => 25605\n                    [post_author] => 5\n                    [post_date] => 2024-12-16 09:12:14\n                    [post_date_gmt] => 2024-12-16 08:12:14\n                    [post_content] => \n                    [post_title] => bam2plot\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bam2plot\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2024-12-18 09:36:22\n                    [post_modified_gmt] => 2024-12-18 08:36:22\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25605\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [9] => WP_Post Object\n                (\n                    [ID] => 24153\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:56\n                    [post_date_gmt] => 2022-11-22 09:25:56\n                    [post_content] => \n                    [post_title] => Bamstats (notsame as BAMstats)\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bamstats-notsame-as-bamstats\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:33:18\n                    [post_modified_gmt] => 2025-05-21 05:33:18\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bamstats-notsame-as-bamstats\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [10] => WP_Post Object\n                (\n                    [ID] => 23785\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:37\n                    [post_date_gmt] => 2022-11-22 09:25:37\n                    [post_content] => \n                    [post_title] => BBMap\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bbmap\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:35:02\n                    [post_modified_gmt] => 2025-05-21 05:35:02\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bbmap\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [11] => WP_Post Object\n                (\n                    [ID] => 24157\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:00\n                    [post_date_gmt] => 2022-11-22 09:26:00\n                    [post_content] => \n                    [post_title] => BCOOL\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bcool\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:35:51\n                    [post_modified_gmt] => 2025-05-21 05:35:51\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bcool\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [12] => WP_Post Object\n                (\n                    [ID] => 24108\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:51\n                    [post_date_gmt] => 2022-11-22 09:25:51\n                    [post_content] => \n                    [post_title] => BELLA\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bella\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:37:24\n                    [post_modified_gmt] => 2025-05-21 05:37:24\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bella\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [13] => WP_Post Object\n                (\n                    [ID] => 24113\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:51\n                    [post_date_gmt] => 2022-11-22 09:25:51\n                    [post_content] => \n                    [post_title] => biohazard-tools\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => biohazard-tools\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:38:41\n                    [post_modified_gmt] => 2025-05-21 05:38:41\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/biohazard-tools\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [14] => WP_Post Object\n                (\n                    [ID] => 23598\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => Blasr\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => blasr\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-04-22 13:25:56\n                    [post_modified_gmt] => 2025-04-22 11:25:56\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/blasr\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [15] => WP_Post Object\n                (\n                    [ID] => 23599\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => blat\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => blat\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:39:14\n                    [post_modified_gmt] => 2025-05-21 05:39:14\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/blat\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [16] => WP_Post Object\n                (\n                    [ID] => 25005\n                    [post_author] => 5\n                    [post_date] => 2023-08-07 08:12:26\n                    [post_date_gmt] => 2023-08-07 06:12:26\n                    [post_content] => \n                    [post_title] => BOLDigger\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => boldigger\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:40:17\n                    [post_modified_gmt] => 2025-05-21 05:40:17\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25005\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [17] => WP_Post Object\n                (\n                    [ID] => 23600\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => Bowtie\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bowtie\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:40:22\n                    [post_modified_gmt] => 2025-05-21 05:40:22\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bowtie\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [18] => WP_Post Object\n                (\n                    [ID] => 23601\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:25:29\n                    [post_date_gmt] => 2022-11-22 09:25:29\n                    [post_content] => \n                    [post_title] => Bowtie2\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => closed\n                    [ping_status] => closed\n                    [post_password] => \n                    [post_name] => bowtie2\n                    [to_ping] => \n                    [pinged] => \n                    [post_modified] => 2025-05-21 07:40:32\n                    [post_modified_gmt] => 2025-05-21 05:40:32\n                    [post_content_filtered] => \n                    [post_parent] => 0\n                    [guid] => http:\/\/bioinfo.genotoul.fr\/index.php\/links\/%link_library_category%\/bowtie2\/\n                    [menu_order] => 0\n                    [post_type] => link_library_links\n                    [post_mime_type] => \n                    [comment_count] => 0\n                    [filter] => raw\n                )\n\n            [19] => WP_Post Object\n                (\n                    [ID] => 24163\n                    [post_author] => 5\n                    [post_date] => 2022-11-22 10:26:06\n                    [post_date_gmt] => 2022-11-22 09:26:06\n                    [post_content] => \n                    [post_title] => BPP\n                    [post_excerpt] => \n                    [post_status] => publish\n                    [comment_status] => 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class=\"LinkLibraryCat LinkLibraryCat1127 level0\"><!-- Div Category --><div id=\"sequences-alignment\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Sequences alignment<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/dulunar\/3rdChimeraMiner\" id=\"link-25351\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">3rdChimeraMiner<\/a>\n<!-- Time to render name section of link id 25351: 3.0994415283203E-6 --> \n<\/td>\n<td>Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data.\n<!-- Time to render link large description section of link id 25351: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_3rdChimeraMiner> How to use <\/a>\n<!-- Time to render notes section of link id 25351: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25351: 0.0001370906829834 --> \n<tr><td><a href=\"https:\/\/github.com\/Maihj\/AC-DIAMOND\/\" id=\"link-23939\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AC-DIAMOND<\/a>\n<!-- Time to render name section of link id 23939: 2.8610229492188E-6 --> \n<\/td>\n<td><p>AC-DIAMOND attempts to speed up DIAMOND via better SIMD parallelization and compressed indexing. Experimental results show that AC-DIAMOND was about 6~7 times faster than DIAMOND on aligning DNA reads or contigs while retaining the essentially the similar sensitivity. AC-DIAMOND was developped based on DIAMOND v0.7.9.<\/p>\n<!-- Time to render link large description section of link id 23939: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23939: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23939: 0.00011420249938965 --> \n<tr><td><a href=\"https:\/\/github.com\/raja-appuswamy\/accel-align-release\" id=\"link-24133\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Accel-align<\/a>\n<!-- Time to render name section of link id 24133: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Accel-align is a fast alignment tool implemented in C++ programming language.<\/p>\n<!-- Time to render link large description section of link id 24133: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24133: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24133: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/phglab\/ALFATClust\" id=\"link-25570\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ALFATClust<\/a>\n<!-- Time to render name section of link id 25570: 3.0994415283203E-6 --> \n<\/td>\n<td>ALignment-Free Adaptive Threshold Clustering:Biological sequence clustering tool with dynamic threshold for individual clusters. Suitable for clustering multiple groups of homologous sequences.\n<!-- Time to render link large description section of link id 25570: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ALFATClust> How to use <\/a>\n<!-- Time to render notes section of link id 25570: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25570: 0.00012087821960449 --> \n<tr><td><a href=\"https:\/\/github.com\/tvandervalk\/AMBER\" id=\"link-25483\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AMBER<\/a>\n<!-- Time to render name section of link id 25483: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Analyzing Mapping Biases and Evaluating Read Reliability.<\/p>\n<!-- Time to render link large description section of link id 25483: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AMBER> How to use <\/a>\n<!-- Time to render notes section of link id 25483: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25483: 0.00020194053649902 --> \n<tr><td><a href=\"https:\/\/github.com\/baoxingsong\/anchorwave\" id=\"link-24859\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AnchorWave<\/a>\n<!-- Time to render name section of link id 24859: 1.9073486328125E-6 --> \n<\/td>\n<td><p>AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals.<\/p>\n<!-- Time to render link large description section of link id 24859: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24859: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24859: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/GDKO\/AvP\" id=\"link-24708\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AvP<\/a>\n<!-- Time to render name section of link id 24708: 2.1457672119141E-6 --> \n<\/td>\n<td><p>AvP performs automatic detection of HGT candidates within a phylogenetic framework.<\/p>\n<!-- Time to render link large description section of link id 24708: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AvP> How to use <\/a>\n<!-- Time to render notes section of link id 24708: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24708: 0.00010323524475098 --> \n<tr><td><a href=\"https:\/\/github.com\/pierrepeterlongo\/back_to_sequences\" id=\"link-25269\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Back_to_sequences<\/a>\n<!-- Time to render name section of link id 25269: 9.5367431640625E-7 --> \n<\/td>\n<td><p>Given a set of kmers (fasta \/ fastq <.gz> format) and a set of sequences (fasta \/ fastq <.gz> format), this tool will extract the sequences containing some of those kmers.<\/p>\n<!-- Time to render link large description section of link id 25269: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Back_to_sequences> How to use <\/a>\n<!-- Time to render notes section of link id 25269: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25269: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/willros\/bam2plot\" id=\"link-25605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bam2plot<\/a>\n<!-- Time to render name section of link id 25605: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Make coverage plots from bam files.<\/p>\n<!-- Time to render link large description section of link id 25605: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bam2plot> How to use <\/a>\n<!-- Time to render notes section of link id 25605: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25605: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/guigolab\/bamstats\" id=\"link-24153\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bamstats (notsame as BAMstats)<\/a>\n<!-- Time to render name section of link id 24153: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bamstats is a command line tool written in Go for computing mapping statistics from a BAM file.<\/p>\n<!-- Time to render link large description section of link id 24153: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24153: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24153: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/bbmap\/\" id=\"link-23785\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BBMap<\/a>\n<!-- Time to render name section of link id 23785: 3.0994415283203E-6 --> \n<\/td>\n<td><p>a short read aligner, as well as various other bioinformatic tools.<\/p>\n<!-- Time to render link large description section of link id 23785: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BBMap> How to use <\/a>\n<!-- Time to render notes section of link id 23785: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23785: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/Malfoy\/BCOOL\" id=\"link-24157\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BCOOL<\/a>\n<!-- Time to render name section of link id 24157: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BCOOL is a read corrector for NGS sequencing data that align reads on a de Bruijn graph.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24157: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24157: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24157: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/giuliaguidi\/bella\" id=\"link-24108\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BELLA<\/a>\n<!-- Time to render name section of link id 24108: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A computationally-efficient and highly-accurate long-read to long-read aligner and overlapper.<\/p>\n<!-- Time to render link large description section of link id 24108: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24108: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24108: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/ustenzel\/biohazard-tools\/src\/master\/\" id=\"link-24113\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">biohazard-tools<\/a>\n<!-- Time to render name section of link id 24113: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This is a collection of command line utilities that do useful stuff involving BAM files for Next Generation Sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24113: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24113: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24113: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/DevNet\/wiki\/Compatible-Software\" id=\"link-23598\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Blasr<\/a>\n<!-- Time to render name section of link id 23598: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Reference-based alignment<\/p>\n<!-- Time to render link large description section of link id 23598: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> ( See SMRTLink) <\/a>\n<!-- Time to render notes section of link id 23598: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23598: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/genome.ucsc.edu\/\" id=\"link-23599\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">blat<\/a>\n<!-- Time to render name section of link id 23599: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The BLAST-Like Alignment Tool: similarity search in databanks. BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.<\/p>\n<!-- Time to render link large description section of link id 23599: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_blat> How to use <\/a>\n<!-- Time to render notes section of link id 23599: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23599: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/DominikBuchner\/BOLDigger\" id=\"link-25005\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BOLDigger<\/a>\n<!-- Time to render name section of link id 25005: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Python program to query .fasta files against the different databases of www.boldsystems.org<\/p>\n<!-- Time to render link large description section of link id 25005: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BOLDigger> How to use <\/a>\n<!-- Time to render notes section of link id 25005: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25005: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\" id=\"link-23600\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bowtie<\/a>\n<!-- Time to render name section of link id 23600: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).<\/p>\n<!-- Time to render link large description section of link id 23600: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bowtie> How to use <\/a>\n<!-- Time to render notes section of link id 23600: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23600: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/index.shtml\" id=\"link-23601\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Bowtie2<\/a>\n<!-- Time to render name section of link id 23601: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.<\/p>\n<!-- Time to render link large description section of link id 23601: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bowtie> How to use <\/a>\n<!-- Time to render notes section of link id 23601: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23601: 0.00010585784912109 --> \n<tr><td><a href=\"https:\/\/github.com\/bpp\/bpp\" id=\"link-24163\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BPP<\/a>\n<!-- Time to render name section of link id 24163: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bayesian analysis of genomic sequence data under the multispecies coalescent model.<\/p>\n<!-- Time to render link large description section of link id 24163: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24163: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24163: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/pellegrini-legacy.mcdb.ucla.edu\/bs_seeker2\/\" id=\"link-24165\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BS-Seeker2-<\/a>\n<!-- Time to render name section of link id 24165: 2.1457672119141E-6 --> \n<\/td>\n<td><p>BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.<\/p>\n<!-- Time to render link large description section of link id 24165: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24165: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24165: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/code.google.com\/p\/bsmap\/\" id=\"link-23602\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BSMAP<\/a>\n<!-- Time to render name section of link id 23602: 1.9073486328125E-6 --> \n<\/td>\n<td><p>BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference<\/p>\n<!-- Time to render link large description section of link id 23602: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23602: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23602: 0.00011992454528809 --> \n<tr><td><a href=\"http:\/\/bio-bwa.sourceforge.net\/\" id=\"link-23603\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwa<\/a>\n<!-- Time to render name section of link id 23603: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.<\/p>\n<!-- Time to render link large description section of link id 23603: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bwa> How to use <\/a>\n<!-- Time to render notes section of link id 23603: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23603: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/bwa-mem2\/bwa-mem2\" id=\"link-24168\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwa-mem2<\/a>\n<!-- Time to render name section of link id 24168: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster.<\/p>\n<!-- Time to render link large description section of link id 24168: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bwa-mem2> How to use <\/a>\n<!-- Time to render notes section of link id 24168: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24168: 0.00011420249938965 --> \n<tr><td><a href=\"https:\/\/github.com\/brentp\/bwa-meth\" id=\"link-24169\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bwa-meth<\/a>\n<!-- Time to render name section of link id 24169: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.<\/p>\n<!-- Time to render link large description section of link id 24169: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bwa-meth> How to use <\/a>\n<!-- Time to render notes section of link id 24169: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24169: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/ComparativeGenomicsToolkit\/cactus\" id=\"link-24984\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cactus<\/a>\n<!-- Time to render name section of link id 24984: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit.<\/p>\n<!-- Time to render link large description section of link id 24984: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Cactus> How to use <\/a>\n<!-- Time to render notes section of link id 24984: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24984: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/estebanpw\/chromeister\" id=\"link-24177\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">chromeister<\/a>\n<!-- Time to render name section of link id 24177: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A dotplot generator for large chromosomes.<\/p>\n<!-- Time to render link large description section of link id 24177: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_chromeister> How to use <\/a>\n<!-- Time to render notes section of link id 24177: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24177: 0.00011706352233887 --> \n<tr><td><a href=\"http:\/\/www.clustal.org\/omega\" id=\"link-23607\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Clustal Omega<\/a>\n<!-- Time to render name section of link id 23607: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks<\/p>\n<!-- Time to render link large description section of link id 23607: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClustalOmega> How to use <\/a>\n<!-- Time to render notes section of link id 23607: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23607: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/clustalw2\/index.html\" id=\"link-23608\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClustalW<\/a>\n<!-- Time to render name section of link id 23608: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Multiple sequence alignment program for DNA or proteins.<\/p>\n<!-- Time to render link large description section of link id 23608: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23608: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23608: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/martin-steinegger\/conterminator\" id=\"link-24800\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Conterminator<\/a>\n<!-- Time to render name section of link id 24800: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Conterminator is an efficient method for detecting incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison.<\/p>\n<!-- Time to render link large description section of link id 24800: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24800: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24800: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/thegenemyers\/DALIGNER\" id=\"link-23613\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DALIGNER<\/a>\n<!-- Time to render name section of link id 23613: 1.9073486328125E-6 --> \n<\/td>\n<td><p>The commands below permit one to find all significant local alignments between reads encoded in Dazzler database. The assumption is that the reads are from a PACBIO RS IIlong read sequencer.<\/p>\n<!-- Time to render link large description section of link id 23613: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23613: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23613: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/bbuchfink\/diamond\" id=\"link-23798\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DIAMOND<\/a>\n<!-- Time to render name section of link id 23798: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Accelerated BLAST compatible local sequence aligner.<\/p>\n<!-- Time to render link large description section of link id 23798: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DIAMOND> How to use <\/a>\n<!-- Time to render notes section of link id 23798: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23798: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/ecoprimers\/wikis\/home\" id=\"link-23617\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ecoPrimers<\/a>\n<!-- Time to render name section of link id 23617: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ecoPrimer is a barcoding software which is written in C language. It finds universal primers from a set of input DNA sequences by finding conserved regions without \"a priori\" on candidate sequences. It also evaluates the quality of the primers and barcode regions by measuring the \"barcode specificity\" and \"barcode coverage\" indices<\/p>\n<!-- Time to render link large description section of link id 23617: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ecoPrimers> How to use <\/a>\n<!-- Time to render notes section of link id 23617: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23617: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/ncbi\/egapx\" id=\"link-25748\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EGAPx<\/a>\n<!-- Time to render name section of link id 25748: 2.1457672119141E-6 --> \n<\/td>\n<td><p>EGAPx is the publicly accessible version of the updated NCBI Eukaryotic Genome Annotation Pipeline.<\/p>\n<!-- Time to render link large description section of link id 25748: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EGAPx> How to use <\/a>\n<!-- Time to render notes section of link id 25748: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25748: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/eggnogdb\/eggnog-mapper\" id=\"link-24209\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eggNog-mapper<\/a>\n<!-- Time to render name section of link id 24209: 2.1457672119141E-6 --> \n<\/td>\n<td><p>eggnog-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only.<\/p>\n<!-- Time to render link large description section of link id 24209: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eggNOG-mapper> How to use <\/a>\n<!-- Time to render notes section of link id 24209: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24209: 0.00011205673217773 --> \n<tr><td><a href=\"https:\/\/github.com\/arshajii\/ema\" id=\"link-24211\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMA<\/a>\n<!-- Time to render name section of link id 24211: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EMA uses a latent variable model to align barcoded short-reads (such as those produced by 10x Genomics' sequencing platform).<\/p>\n<!-- Time to render link large description section of link id 24211: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24211: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24211: 0.00011801719665527 --> \n<tr><td><a href=\"http:\/\/emboss.sourceforge.net\/\" id=\"link-23882\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EMBOSS<\/a>\n<!-- Time to render name section of link id 23882: 1.9073486328125E-6 --> \n<\/td>\n<td><p>EMBOSS is \"The European Molecular Biology Open Software Suite\". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.<\/p>\n<!-- Time to render link large description section of link id 23882: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EMBOSS> How to use <\/a>\n<!-- Time to render notes section of link id 23882: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23882: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/www.ebi.ac.uk\/about\/vertebrate-genomics\/software\/exonerate\" id=\"link-23621\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Exonerate<\/a>\n<!-- Time to render name section of link id 23621: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A generic tool for sequence alignment.<\/p>\n<!-- Time to render link large description section of link id 23621: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Exonerate> How to use <\/a>\n<!-- Time to render notes section of link id 23621: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23621: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/refresh-bio\/FAMSA\" id=\"link-24043\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FAMSA<\/a>\n<!-- Time to render name section of link id 24043: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM)<\/p>\n<!-- Time to render link large description section of link id 24043: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24043: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24043: 0.00011515617370605 --> \n<tr><td><a href=\"https:\/\/fasta.bioch.virginia.edu\/fasta_www2\/fasta_list2.shtml\" id=\"link-23623\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FASTA<\/a>\n<!-- Time to render name section of link id 23623: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FASTA is a sequence similarity search tool which uses heuristics for fast local alignment searching.<\/p>\n<!-- Time to render link large description section of link id 23623: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FASTA> How to use <\/a>\n<!-- Time to render notes section of link id 23623: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23623: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/ParBLiSS\/FastANI\" id=\"link-24124\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FastANI<\/a>\n<!-- Time to render name section of link id 24124: 1.9073486328125E-6 --> \n<\/td>\n<td><p>FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)<\/p>\n<!-- Time to render link large description section of link id 24124: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FastANI> How to use <\/a>\n<!-- Time to render notes section of link id 24124: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24124: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/schneebergerlab\/fixchr\" id=\"link-24970\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fixchr<\/a>\n<!-- Time to render name section of link id 24970: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This package selects homologous chromosomes between two genomes by comparing whole-genome alignments between them. Additionally, it generates dotplots for quick checking of the output.<\/p>\n<!-- Time to render link large description section of link id 24970: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_fixchr> How to use <\/a>\n<!-- Time to render notes section of link id 24970: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24970: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/natir\/fpa\" id=\"link-24101\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">fpa<\/a>\n<!-- Time to render name section of link id 24101: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Filter Pairwise Alignment<\/p>\n<!-- Time to render link large description section of link id 24101: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24101: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24101: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/marschall-lab\/gaftools\" id=\"link-26161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gaftools<\/a>\n<!-- Time to render name section of link id 26161: 2.1457672119141E-6 --> \n<\/td>\n<td><p>gaftools is a fast and comprehensive toolkit designed for processing pangenome alignments.<\/p>\n<!-- Time to render link large description section of link id 26161: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gaftools> How to use <\/a>\n<!-- Time to render notes section of link id 26161: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26161: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/gemlibrary\/\" id=\"link-25030\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GEM-library<\/a>\n<!-- Time to render name section of link id 25030: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of very optimized tools for indexing\/querying huge genomes\/files.<\/p>\n<!-- Time to render link large description section of link id 25030: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GEM-library> How to use <\/a>\n<!-- Time to render notes section of link id 25030: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25030: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/BrendelGroup\/GeneSeqer\" id=\"link-24247\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GeneSeqer<\/a>\n<!-- Time to render name section of link id 24247: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Sensitive spliced-alignment of cDNAs or proteins.<\/p>\n<!-- Time to render link large description section of link id 24247: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24247: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24247: 0.0001060962677002 --> \n<tr><td><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/Wise2\/index.html\" id=\"link-23768\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Genewise<\/a>\n<!-- Time to render name section of link id 23768: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Wise2 is a package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence.<\/p>\n<!-- Time to render link large description section of link id 23768: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Genewise> How to use <\/a>\n<!-- Time to render notes section of link id 23768: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23768: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/cpockrandt\/genmap\" id=\"link-25923\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenMap<\/a>\n<!-- Time to render name section of link id 25923: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast and Exact Computation of Genome Mappability.<\/p>\n<!-- Time to render link large description section of link id 25923: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GenMap> How to use <\/a>\n<!-- Time to render notes section of link id 25923: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25923: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/seqoccin\/GenomOrder\" id=\"link-24249\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomOrder<\/a>\n<!-- Time to render name section of link id 24249: 2.1457672119141E-6 --> \n<\/td>\n<td><p>GenomOrder is a Nextflow pipeline reordering and renaming scaffolds from up to 5 assemblies using a reference. It is also able to produce D-Genies back-up files allowing rapid visual comparison of chromosomes of the assemblies versus the reference. These files can be uploaded and visualized with the online tool D-Genies : http:\/\/dgenies.toulouse.inra.fr\/ The assembly mapping versus the reference is performed with minimap2. These assemblies can be scaffolded or not. If they are not, an option enables to scaffold them according to the reference. The pipeline produces D-Genies back-up file for a user defined list of reference chromosomes. The chromosome file contains one reference chromosome name per line.<\/p>\n<!-- Time to render link large description section of link id 24249: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24249: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24249: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/research-pub.gene.com\/gmap\/\" id=\"link-23638\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GMAP-GSNAP<\/a>\n<!-- Time to render name section of link id 23638: 3.0994415283203E-6 --> \n<\/td>\n<td><p>GMAP: A Genomic Mapping and Alignment Program for mRNA and EST SequencesGSNAP: Genomic Short-read Nucleotide Alignment Program<\/p>\n<!-- Time to render link large description section of link id 23638: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GMAP-GSNAP> How to use <\/a>\n<!-- Time to render notes section of link id 23638: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23638: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/evolbioinfo\/goalign\" id=\"link-24259\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Goalign<\/a>\n<!-- Time to render name section of link id 24259: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Goalign is a set of command line tools to manipulate multiple alignments.<\/p>\n<!-- Time to render link large description section of link id 24259: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Goalign> How to use <\/a>\n<!-- Time to render notes section of link id 24259: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24259: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/maickrau\/GraphAligner\" id=\"link-24261\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphAligner<\/a>\n<!-- Time to render name section of link id 24261: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Seed-and-extend program for aligning long error-prone reads to genome graphs.<\/p>\n<!-- Time to render link large description section of link id 24261: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GraphAligner> How to use <\/a>\n<!-- Time to render notes section of link id 24261: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24261: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/isovic\/graphmap\" id=\"link-24262\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GraphMap<\/a>\n<!-- Time to render name section of link id 24262: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A highly sensitive and accurate mapper for long, error-prone reads.<\/p>\n<!-- Time to render link large description section of link id 24262: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24262: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24262: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/hsinnan75\/GSAlign\" id=\"link-24265\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GSAlign<\/a>\n<!-- Time to render name section of link id 24265: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An ultra-fast sequence alignment algorithm for intra-species genome comparison.<\/p>\n<!-- Time to render link large description section of link id 24265: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GSAlign> How to use <\/a>\n<!-- Time to render notes section of link id 24265: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24265: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/harvest-tools\" id=\"link-25350\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HarvestTools<\/a>\n<!-- Time to render name section of link id 25350: 2.1457672119141E-6 --> \n<\/td>\n<td><p>HarvestTools is a utility for creating and interfacing with Gingr files, which are efficient archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.<\/p>\n<!-- Time to render link large description section of link id 25350: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HarvestTools> How to use <\/a>\n<!-- Time to render notes section of link id 25350: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25350: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/daehwankimlab.github.io\/hisat2\/\" id=\"link-23921\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HISAT2<\/a>\n<!-- Time to render name section of link id 23921: 2.8610229492188E-6 --> \n<\/td>\n<td><p>HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).<\/p>\n<!-- Time to render link large description section of link id 23921: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HISAT2> How to use <\/a>\n<!-- Time to render notes section of link id 23921: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23921: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/VIB-PSB\/i-ADHoRe\" id=\"link-24994\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">i-ADHoRe<\/a>\n<!-- Time to render name section of link id 24994: 2.1457672119141E-6 --> \n<\/td>\n<td><p>i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.<\/p>\n<!-- Time to render link large description section of link id 24994: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_i-ADHoRe> How to use <\/a>\n<!-- Time to render notes section of link id 24994: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24994: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/ridgelab\/JustOrthologs\" id=\"link-23976\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">JustOrthologs<\/a>\n<!-- Time to render name section of link id 23976: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A Fast, Accurate, and User-Friendly Ortholog-Finding Algorithm<\/p>\n<!-- Time to render link large description section of link id 23976: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23976: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23976: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/kma\" id=\"link-24114\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KMA<\/a>\n<!-- Time to render name section of link id 24114: 2.1457672119141E-6 --> \n<\/td>\n<td><p>KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.<\/p>\n<!-- Time to render link large description section of link id 24114: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KMA> How to use <\/a>\n<!-- Time to render notes section of link id 24114: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24114: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/mcfrith\/last\" id=\"link-23654\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LAST<\/a>\n<!-- Time to render name section of link id 23654: 2.1457672119141E-6 --> \n<\/td>\n<td><p>LAST finds similar regions between sequences.<\/p>\n<!-- Time to render link large description section of link id 23654: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LAST> How to use <\/a>\n<!-- Time to render notes section of link id 23654: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23654: 0.00011396408081055 --> \n<tr><td><a href=\"https:\/\/github.com\/faylward\/lastp_aai\" id=\"link-24342\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">lastp_aai<\/a>\n<!-- Time to render name section of link id 24342: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A simple Python script for calculating pairwise amino acid identity (AAI) between protein files (extension .faa)<\/p>\n<!-- Time to render link large description section of link id 24342: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24342: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24342: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.bx.psu.edu\/miller_lab\/dist\/README.lastz-1.02.00\/README.lastz-1.02.00a.html#install\" id=\"link-23852\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LASTZ<\/a>\n<!-- Time to render name section of link id 23852: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically.<\/p>\n<!-- Time to render link large description section of link id 23852: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LASTZ> How to use <\/a>\n<!-- Time to render notes section of link id 23852: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23852: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/leeHom\" id=\"link-24344\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">leeHom<\/a>\n<!-- Time to render name section of link id 24344: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A program for the Bayesian reconstruction of ancient DNA.<\/p>\n<!-- Time to render link large description section of link id 24344: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24344: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24344: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/bioweb.supagro.inra.fr\/macse\/\" id=\"link-24361\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MACSE<\/a>\n<!-- Time to render name section of link id 24361: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons: a wide range of molecular analyses relies on multiple sequence alignments (MSA).<\/p>\n<!-- Time to render link large description section of link id 24361: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24361: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24361: 0.00010991096496582 --> \n<tr><td><a href=\"http:\/\/mafft.cbrc.jp\/alignment\/software\/\" id=\"link-23658\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAFFT<\/a>\n<!-- Time to render name section of link id 23658: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MAFFT is a multiple sequence alignment program for unix-like operating systems.\u00a0 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of &lt;?200 sequences), FFT-NS-2 (fast; for alignment of &lt;?10,000 sequences), <i>etc<\/i>.<\/p>\n<!-- Time to render link large description section of link id 23658: 6.9141387939453E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAFFT> How to use <\/a>\n<!-- Time to render notes section of link id 23658: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23658: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/ncbi.github.io\/magicblast\/\" id=\"link-24363\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Magic-BLAST<\/a>\n<!-- Time to render name section of link id 24363: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.<\/p>\n<!-- Time to render link large description section of link id 24363: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Magic-BLAST> How to use <\/a>\n<!-- Time to render notes section of link id 24363: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24363: 0.00011491775512695 --> \n<tr><td><a href=\"http:\/\/ab.inf.uni-tuebingen.de\/software\/malt\/\" id=\"link-24057\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MALT<\/a>\n<!-- Time to render name section of link id 24057: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MALT (MEGAN alignment tool) is an extension of MEGAN (metagenome analyzer).<br \/>\r\nMALT performs alignment of metagenomic reads against a database of reference sequences (such as NR, GenBank or Silva) and produces a MEGAN RMA file as output. The software is currently under development.<\/p>\n<!-- Time to render link large description section of link id 24057: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MALT> How to use <\/a>\n<!-- Time to render notes section of link id 24057: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24057: 0.00011301040649414 --> \n<tr><td><a href=\"http:\/\/www.netlab.uky.edu\/p\/bioinfo\/MapSplice\" id=\"link-23660\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MapSplice<\/a>\n<!-- Time to render name section of link id 23660: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Accurate mapping of RNA-seq reads for splice junction discovery.<\/p>\n<!-- Time to render link large description section of link id 23660: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23660: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23660: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/MashMap\" id=\"link-24367\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MashMap<\/a>\n<!-- Time to render name section of link id 24367: 2.1457672119141E-6 --> \n<\/td>\n<td><p>MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. \u00a0It can be useful for mapping genome assembly or long reads (PacBio\/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, Mashmap computes alignment boundaries and identity estimates using\u00a0k-mers. It does not compute the alignments explicitly, but rather estimates a\u00a0k-mer based\u00a0Jaccard similarity\u00a0using a combination of\u00a0Minimizers\u00a0and\u00a0MinHash. This is then converted to an estimate of sequence identity using the\u00a0Mash distance.\u00a0<\/p>\n<!-- Time to render link large description section of link id 24367: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24367: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24367: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/wyp1125\/MCScanX\" id=\"link-24369\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MCScanX<\/a>\n<!-- Time to render name section of link id 24369: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MCScan is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors.<\/p>\n<!-- Time to render link large description section of link id 24369: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MCScanX> How to use <\/a>\n<!-- Time to render notes section of link id 24369: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24369: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/xiaochuanle\/MECAT\" id=\"link-23979\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MECAT<\/a>\n<!-- Time to render name section of link id 23979: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads.<\/p>\n<!-- Time to render link large description section of link id 23979: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23979: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23979: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/github.com\/DiltheyLab\/MetaMaps\" id=\"link-23971\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MetaMaps<\/a>\n<!-- Time to render name section of link id 23971: 2.8610229492188E-6 --> \n<\/td>\n<td><p>MetaMaps is tool specifically developed for the analysis of long-read (PacBio\/ONT) metagenomic datasets. It simultaenously carries out read assignment and sample composition estimation. It is faster than classical exact alignment-based approaches, and its output is more information-rich than that of kmer-spectra-based methods. For example, each MetaMaps alignment comes with an approximate alignment location, an estimated alignment identity and a mapping quality.<\/p>\n<!-- Time to render link large description section of link id 23971: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23971: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23971: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/metagenopolis\/meteor\" id=\"link-24891\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">meteor<\/a>\n<!-- Time to render name section of link id 24891: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Meteor (Metagenomic Explorator), a software for profiling metagenomic data at gene level.<\/p>\n<!-- Time to render link large description section of link id 24891: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_meteor> How to use <\/a>\n<!-- Time to render notes section of link id 24891: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24891: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/minigraph\" id=\"link-24381\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minigraph<\/a>\n<!-- Time to render name section of link id 24381: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Minigraph is a sequence-to-graph mapper and graph constructor.<\/p>\n<!-- Time to render link large description section of link id 24381: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minigraph> How to use <\/a>\n<!-- Time to render notes section of link id 24381: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24381: 0.00011587142944336 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/minimap\" id=\"link-23811\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Minimap<\/a>\n<!-- Time to render name section of link id 23811: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Experimental tool to find approximate mapping positions between long sequences<\/p>\n<!-- Time to render link large description section of link id 23811: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Minimap> How to use <\/a>\n<!-- Time to render notes section of link id 23811: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23811: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/lh3\/miniprot\" id=\"link-24385\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Miniprot<\/a>\n<!-- Time to render name section of link id 24385: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Aligning proteins to genomes with splicing and frameshift.<\/p>\n<!-- Time to render link large description section of link id 24385: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Miniprot> How to use <\/a>\n<!-- Time to render notes section of link id 24385: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24385: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/GfellerLab\/MixMHCpred\" id=\"link-25489\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MixMHCpred<\/a>\n<!-- Time to render name section of link id 25489: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A pan-Allele predictor designed for predicting peptide bindings to MHC alleles and can also perform sequence alignment and binding motif plotting.<\/p>\n<!-- Time to render link large description section of link id 25489: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MixMHCpred> How to use <\/a>\n<!-- Time to render notes section of link id 25489: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25489: 0.00019216537475586 --> \n<tr><td><a href=\"https:\/\/github.com\/soedinglab\/MMseqs2\" id=\"link-24097\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MMseqs2<\/a>\n<!-- Time to render name section of link id 24097: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge proteins\/nucleotide sequence sets.<\/p>\n<!-- Time to render link large description section of link id 24097: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MMseqs2> How to use <\/a>\n<!-- Time to render notes section of link id 24097: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24097: 0.00011420249938965 --> \n<tr><td><a href=\"https:\/\/code.google.com\/p\/mosaik-aligner\/\" id=\"link-23670\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MOSAIK<\/a>\n<!-- Time to render name section of link id 23670: 1.9073486328125E-6 --> \n<\/td>\n<td><p><strong>MOSAIK<\/strong> is a reference-guided assembler comprising of two main modular programs<\/p>\n<!-- Time to render link large description section of link id 23670: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23670: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23670: 0.00012898445129395 --> \n<tr><td><a href=\"http:\/\/mugsy.sourceforge.net\/\" id=\"link-24401\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mugsy<\/a>\n<!-- Time to render name section of link id 24401: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome. Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 2011 27(3):334-4<\/p>\n<!-- Time to render link large description section of link id 24401: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Mugsy> How to use <\/a>\n<!-- Time to render notes section of link id 24401: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24401: 0.00011301040649414 --> \n<tr><td><a href=\"http:\/\/multalin.toulouse.inra.fr\/multalin\/multalin.html\" id=\"link-23675\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MultAlin<\/a>\n<!-- Time to render name section of link id 23675: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Multiple sequence alignment <a name=\"sequence_input_format\"><\/a>with hierarchical clustering.<b><\/b><\/p>\n<!-- Time to render link large description section of link id 23675: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23675: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23675: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/mummer4\/mummer\" id=\"link-23676\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MUMmer<\/a>\n<!-- Time to render name section of link id 23676: 1.9073486328125E-6 --> \n<\/td>\n<td><p>MUMmer is a package for rapidly aligning <b>entire genomes<\/b>, whether in complete or draft form.<\/p>\n<!-- Time to render link large description section of link id 23676: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MUMmer> How to use <\/a>\n<!-- Time to render notes section of link id 23676: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23676: 0.00011587142944336 --> \n<tr><td><a href=\"http:\/\/www.drive5.com\/muscle\/\" id=\"link-23677\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MUSCLE<\/a>\n<!-- Time to render name section of link id 23677: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Multiple sequence alignment (nucleic or proteic).<\/p>\n<!-- Time to render link large description section of link id 23677: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MUSCLE> How to use <\/a>\n<!-- Time to render notes section of link id 23677: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23677: 0.00011396408081055 --> \n<tr><td><a href=\"http:\/\/blast.ncbi.nlm.nih.gov\" id=\"link-23679\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_Blast<\/a>\n<!-- Time to render name section of link id 23679: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Similarity search against databanks.<\/p>\n<!-- Time to render link large description section of link id 23679: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_Blast> How to use <\/a>\n<!-- Time to render notes section of link id 23679: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23679: 0.00011396408081055 --> \n<tr><td><a href=\"http:\/\/blast.ncbi.nlm.nih.gov\" id=\"link-23868\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NCBI_Blast+<\/a>\n<!-- Time to render name section of link id 23868: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Similarity search against databanks.<\/p>\n<!-- Time to render link large description section of link id 23868: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NCBI_Blast+> How to use <\/a>\n<!-- Time to render notes section of link id 23868: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23868: 0.00010204315185547 --> \n<tr><td><a href=\"https:\/\/github.com\/philres\/ngmlr\" id=\"link-24037\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NGMLR<\/a>\n<!-- Time to render name section of link id 24037: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations SV detection from paired end reads mapping<\/p>\n<!-- Time to render link large description section of link id 24037: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NGMLR> How to use <\/a>\n<!-- Time to render notes section of link id 24037: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24037: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/MikkelSchubert\/paleomix\/wiki\/Overview\" id=\"link-23684\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PALEOMIX<\/a>\n<!-- Time to render name section of link id 23684: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The PALEOMIX pipeline is a set of free and open-source pipelines and tools designed to enable the rapid processing of Next Generation Sequencing (NGS) data, starting from de-multiplexed reads from one or more samples, through sequence processing and alignment, and ending with genotyping, phylogenetic inference on the samples, as well as metagenomic analysis of the samples.<\/p>\n<!-- Time to render link large description section of link id 23684: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PALEOMIX> How to use <\/a>\n<!-- Time to render notes section of link id 23684: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23684: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/paragraph\" id=\"link-24430\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Paragraph<\/a>\n<!-- Time to render name section of link id 24430: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Graph realignment tools for structural variants.<\/p>\n<!-- Time to render link large description section of link id 24430: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Paragraph> How to use <\/a>\n<!-- Time to render notes section of link id 24430: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24430: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/parsnp\" id=\"link-24971\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Parsnp<\/a>\n<!-- Time to render name section of link id 24971: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.<\/p>\n<!-- Time to render link large description section of link id 24971: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Parsnp> How to use <\/a>\n<!-- Time to render notes section of link id 24971: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24971: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/smirarab\/pasta\" id=\"link-24116\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PASTA<\/a>\n<!-- Time to render name section of link id 24116: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PASTA estimates alignments and ML trees from unaligned sequences using an iterative approach. In each iteration, it first estimates a multiple sequence alignment using the current tree as a guide and then estimates an ML tree on (a masked version of) the alignment.<\/p>\n<!-- Time to render link large description section of link id 24116: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PASTA> How to use <\/a>\n<!-- Time to render notes section of link id 24116: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24116: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/icebert.github.io\/pblat\/\" id=\"link-24435\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pblat<\/a>\n<!-- Time to render name section of link id 24435: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Parallelized blat with multi-threads support.<\/p>\n<!-- Time to render link large description section of link id 24435: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pblat> How to use <\/a>\n<!-- Time to render notes section of link id 24435: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24435: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/PacificBiosciences\/pbmm2\" id=\"link-25904\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pbmm2<\/a>\n<!-- Time to render name section of link id 25904: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A minimap2 frontend for PacBio native data format.<\/p>\n<!-- Time to render link large description section of link id 25904: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pbmm2> How to use <\/a>\n<!-- Time to render notes section of link id 25904: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25904: 9.7990036010742E-5 --> \n<tr><td><a href=\"http:\/\/broadinstitute.github.io\/picard\/\" id=\"link-23694\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">picard-tools<\/a>\n<!-- Time to render name section of link id 23694: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.<\/p>\n<!-- Time to render link large description section of link id 23694: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_picard-tools> How to use <\/a>\n<!-- Time to render notes section of link id 23694: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23694: 0.0001220703125 --> \n<tr><td><a href=\"https:\/\/plast.inria.fr\" id=\"link-23697\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PLAST<\/a>\n<!-- Time to render name section of link id 23697: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.<\/p>\n<!-- Time to render link large description section of link id 23697: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23697: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23697: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/ariloytynoja.github.io\/prank-msa\/\" id=\"link-24048\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PRANK<\/a>\n<!-- Time to render name section of link id 24048: 2.1457672119141E-6 --> \n<\/td>\n<td><p>PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.<\/p>\n<!-- Time to render link large description section of link id 24048: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PRANK> How to use <\/a>\n<!-- Time to render notes section of link id 24048: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24048: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/probcons.stanford.edu\/about.html\" id=\"link-24462\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PROBCONSRNA<\/a>\n<!-- Time to render name section of link id 24462: 2.8610229492188E-6 --> \n<\/td>\n<td><p>PROBCONS is a tool for generating multiple alignments of protein sequences.<\/p>\n<!-- Time to render link large description section of link id 24462: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24462: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24462: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/glennhickey\/progressiveCactus\" id=\"link-23953\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProgressiveCactus<\/a>\n<!-- Time to render name section of link id 23953: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Progressive Cactus is a whole-genome alignment package.<\/p>\n<!-- Time to render link large description section of link id 23953: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23953: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23953: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/gatech-genemark\/ProtHint\" id=\"link-24464\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ProtHint<\/a>\n<!-- Time to render name section of link id 24464: 1.9073486328125E-6 --> \n<\/td>\n<td><p>ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.<\/p>\n<!-- Time to render link large description section of link id 24464: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ProtHint> How to use <\/a>\n<!-- Time to render notes section of link id 24464: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24464: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/pufferfish\" id=\"link-24468\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Puffaligner<\/a>\n<!-- Time to render name section of link id 24468: 9.5367431640625E-7 --> \n<\/td>\n<td><p>Puffaligner is a fast, sensitive and accurate aligner built on top of the Pufferfish index.<\/p>\n<!-- Time to render link large description section of link id 24468: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24468: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24468: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/code.google.com\/p\/pysam\" id=\"link-23702\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pysam<\/a>\n<!-- Time to render name section of link id 23702: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the <a href=\"http:\/\/samtools.sourceforge.net\/\" rel=\"nofollow\">samtools<\/a> C-API.<\/p>\n<!-- Time to render link large description section of link id 23702: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23702: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23702: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/alimanfoo\/pysamstats\" id=\"link-26218\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pysamstats<\/a>\n<!-- Time to render name section of link id 26218: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file.<\/p>\n<!-- Time to render link large description section of link id 26218: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pysamstats> How to use <\/a>\n<!-- Time to render notes section of link id 26218: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26218: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/freezer333\/qgrs-cpp\" id=\"link-24473\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">qgrs-cpp<\/a>\n<!-- Time to render name section of link id 24473: 2.1457672119141E-6 --> \n<\/td>\n<td><p>C++ implementation of QGRS mapping algorithm (QGRS Mapper is a software program that generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences.)<\/p>\n<!-- Time to render link large description section of link id 24473: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24473: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24473: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/qualimap.bioinfo.cipf.es\/\" id=\"link-23705\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Qualimap<\/a>\n<!-- Time to render name section of link id 23705: 2.1457672119141E-6 --> \n<\/td>\n<td><p><b>Qualimap 2<\/b> is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.<\/p>\n<!-- Time to render link large description section of link id 23705: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Qualimap> How to use <\/a>\n<!-- Time to render notes section of link id 23705: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23705: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/ctlab\/quant3p\" id=\"link-24475\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">quant3p<\/a>\n<!-- Time to render name section of link id 24475: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A set of scripts for 3' RNA-seq quantification.<\/p>\n<!-- Time to render link large description section of link id 24475: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_quant3p> How to use <\/a>\n<!-- Time to render notes section of link id 24475: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24475: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/DessimozLab\/read2tree\" id=\"link-24959\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">read2tree<\/a>\n<!-- Time to render name section of link id 24959: 1.9073486328125E-6 --> \n<\/td>\n<td><p>read2tree is a software tool that allows to obtain alignment matrices for tree inference.<\/p>\n<!-- Time to render link large description section of link id 24959: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_read2tree> How to use <\/a>\n<!-- Time to render notes section of link id 24959: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24959: 0.0001060962677002 --> \n<tr><td><a href=\"http:\/\/younglab.wi.mit.edu\/super_enhancer_code.html\" id=\"link-24504\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ROSE<\/a>\n<!-- Time to render name section of link id 24504: 2.1457672119141E-6 --> \n<\/td>\n<td><p>To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)<\/p>\n<!-- Time to render link large description section of link id 24504: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ROSE> How to use <\/a>\n<!-- Time to render notes section of link id 24504: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24504: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/salmon\" id=\"link-23776\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Salmon<\/a>\n<!-- Time to render name section of link id 23776: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Highly-accurate &amp; wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments<\/p>\n<!-- Time to render link large description section of link id 23776: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Salmon> How to use <\/a>\n<!-- Time to render notes section of link id 23776: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23776: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/GregoryFaust\/samblaster\" id=\"link-23829\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samblaster<\/a>\n<!-- Time to render name section of link id 23829: 1.9073486328125E-6 --> \n<\/td>\n<td><p>samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and\/or split read mappings to separate SAM files, and\/or unmapped\/clipped reads to a separate FASTQ file.<\/p>\n<!-- Time to render link large description section of link id 23829: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_samblaster> How to use <\/a>\n<!-- Time to render notes section of link id 23829: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23829: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/github.com\/tseemann\/samclip\" id=\"link-24508\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samclip<\/a>\n<!-- Time to render name section of link id 24508: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Filter SAM file for soft and hard clipped alignments<\/p>\n<!-- Time to render link large description section of link id 24508: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24508: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24508: 0.00011420249938965 --> \n<tr><td><a href=\"http:\/\/samtools.sourceforge.net\/\" id=\"link-23721\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">samtools<\/a>\n<!-- Time to render name section of link id 23721: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SAM (Sequence Alignment\/Map). SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.<\/p>\n<!-- Time to render link large description section of link id 23721: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_samtools> How to use <\/a>\n<!-- Time to render notes section of link id 23721: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23721: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/satsuma.sourceforge.net\/\" id=\"link-24509\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Satsuma<\/a>\n<!-- Time to render name section of link id 24509: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Highly sensitive whole-genome synteny alignments.<\/p>\n<!-- Time to render link large description section of link id 24509: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24509: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24509: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/AntonelliLab\/seqcap_processor\" id=\"link-24513\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SECAPR<\/a>\n<!-- Time to render name section of link id 24513: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Used to process targeted sequencing (or Gene capture) data by applying assembly and subsequent mapping algorithms (reducing paralogs unlike Hybpiper).<\/p>\n<!-- Time to render link large description section of link id 24513: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24513: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24513: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/www.bioinf.uni-leipzig.de\/Software\/segemehl\/\" id=\"link-24677\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">segemehl<\/a>\n<!-- Time to render name section of link id 24677: 3.0994415283203E-6 --> \n<\/td>\n<td><p>segemehl is a software to map short sequencer reads to reference genomes. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).<\/p>\n<!-- Time to render link large description section of link id 24677: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24677: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24677: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/guertinlab.github.io\/seqOutBias\/\" id=\"link-26133\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqOutBias<\/a>\n<!-- Time to render name section of link id 26133: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Universal correction of enzymatic sequence bias.<\/p>\n<!-- Time to render link large description section of link id 26133: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqOutBias> How to use <\/a>\n<!-- Time to render notes section of link id 26133: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26133: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/seqwish\" id=\"link-24515\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">seqwish<\/a>\n<!-- Time to render name section of link id 24515: 2.1457672119141E-6 --> \n<\/td>\n<td><p>seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments.<\/p>\n<!-- Time to render link large description section of link id 24515: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_seqwish> How to use <\/a>\n<!-- Time to render notes section of link id 24515: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24515: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/ChrisHIV\/shiver\" id=\"link-24670\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">shiver<\/a>\n<!-- Time to render name section of link id 24670: 2.1457672119141E-6 --> \n<\/td>\n<td><p>shiver is a tool for mapping paired-end short reads to a custom reference sequence constructed using do novo assembled contigs, in order to minimise the biased loss of information that occurs from mapping to a reference that differs from the sample.<\/p>\n<!-- Time to render link large description section of link id 24670: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24670: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24670: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/compbio.cs.toronto.edu\/shrimp\/\" id=\"link-24088\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SHRiMP<\/a>\n<!-- Time to render name section of link id 24088: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.<\/p>\n<!-- Time to render link large description section of link id 24088: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24088: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24088: 0.00010776519775391 --> \n<tr><td><a href=\"https:\/\/github.com\/medvedevgroup\/SibeliaZ\" id=\"link-24517\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SibeliaZ<\/a>\n<!-- Time to render name section of link id 24517: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SibeliaZ is a whole-genome alignment and locally-coliinear blocks construction pipeline. The blocks coordinates are output in GFF format and the alignment is in MAF.<\/p>\n<!-- Time to render link large description section of link id 24517: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SibeliaZ> How to use <\/a>\n<!-- Time to render notes section of link id 24517: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24517: 0.00010585784912109 --> \n<tr><td><a href=\"http:\/\/lbbe.univ-lyon1.fr\/Overview.html?lang=fr\" id=\"link-23914\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Silix<\/a>\n<!-- Time to render name section of link id 23914: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.<\/p>\n<!-- Time to render link large description section of link id 23914: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SiLiX> How to use <\/a>\n<!-- Time to render notes section of link id 23914: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23914: 0.00011086463928223 --> \n<tr><td><a href=\"https:\/\/www.ebi.ac.uk\/research\/goldman\/software\/slr\/\" id=\"link-24090\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SLR<\/a>\n<!-- Time to render name section of link id 24090: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SLR is a program to detect sites in coding DNA that are unusually conserved and\/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree.<\/p>\n<!-- Time to render link large description section of link id 24090: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SLR> How to use <\/a>\n<!-- Time to render notes section of link id 24090: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24090: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/www.sanger.ac.uk\/science\/tools\/smalt-0\" id=\"link-24031\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SMALT<\/a>\n<!-- Time to render name section of link id 24031: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SMALT aligns DNA sequencing reads with a reference genome.<\/p>\r\n<p>Reads from a wide range of sequencing platforms can be processed, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads are supported. There is no support for SOLiD reads.<\/p>\n<!-- Time to render link large description section of link id 24031: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24031: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24031: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/ogotoh\/spaln\" id=\"link-24531\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Spaln<\/a>\n<!-- Time to render name section of link id 24531: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.<\/p>\n<!-- Time to render link large description section of link id 24531: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Spaln> How to use <\/a>\n<!-- Time to render notes section of link id 24531: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24531: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/hall-lab\/speedseq\" id=\"link-24128\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpeedSeq<\/a>\n<!-- Time to render name section of link id 24128: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A flexible framework for rapid genome analysis and interpretation.<\/p>\n<!-- Time to render link large description section of link id 24128: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24128: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24128: 0.0001060962677002 --> \n<tr><td><a href=\"https:\/\/github.com\/rvaser\/spoa\" id=\"link-24534\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Spoa<\/a>\n<!-- Time to render name section of link id 24534: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A multiple sequence alignment tool\/library that implements the POA (partial order alignement) algorithm using SIMD.<\/p>\n<!-- Time to render link large description section of link id 24534: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24534: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24534: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/marekborowiec\/spruceup\" id=\"link-24536\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">spruceup<\/a>\n<!-- Time to render name section of link id 24536: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tools to discover, visualize, and remove outlier sequences in large multiple sequence alignments.<\/p>\n<!-- Time to render link large description section of link id 24536: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24536: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24536: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/jtamames\/SqueezeMeta\" id=\"link-25492\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SqueezeMeta<\/a>\n<!-- Time to render name section of link id 25492: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fully automated metagenomics pipeline, from reads to bins.<\/p>\n<!-- Time to render link large description section of link id 25492: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SqueezeMeta> How to use <\/a>\n<!-- Time to render notes section of link id 25492: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25492: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/mzytnicki\/srnaMapper\" id=\"link-24541\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">srnaMapper<\/a>\n<!-- Time to render name section of link id 24541: 2.1457672119141E-6 --> \n<\/td>\n<td><p>This tool maps reads produced by sRNA-Seq to a genome.<\/p>\n<!-- Time to render link large description section of link id 24541: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24541: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24541: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/alexdobin\/STAR\" id=\"link-23912\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STAR<\/a>\n<!-- Time to render name section of link id 23912: 1.9073486328125E-6 --> \n<\/td>\n<td><p><span class=\"col-11 text-gray-dark mr-2\">RNA-seq aligner<\/span><\/p>\n<!-- Time to render link large description section of link id 23912: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_STAR> How to use <\/a>\n<!-- Time to render notes section of link id 23912: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23912: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/ksahlin\/StrobeAlign\" id=\"link-24544\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">StrobeAlign<\/a>\n<!-- Time to render name section of link id 24544: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Aligns short reads using dynamic seed size with strobemers.<\/p>\n<!-- Time to render link large description section of link id 24544: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24544: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24544: 0.00011301040649414 --> \n<tr><td><a href=\"http:\/\/bioinf.wehi.edu.au\/subread-package\/\" id=\"link-23743\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Subread<\/a>\n<!-- Time to render name section of link id 23743: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool kit for processing next-gen sequencing data<\/p>\n<!-- Time to render link large description section of link id 23743: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Subread> How to use <\/a>\n<!-- Time to render notes section of link id 23743: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23743: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/git.metabarcoding.org\/obitools\/sumaclust\" id=\"link-23973\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sumaclust<\/a>\n<!-- Time to render name section of link id 23973: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Fast and exact clustering of sequences.<\/p>\n<!-- Time to render link large description section of link id 23973: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sumaclust> How to use <\/a>\n<!-- Time to render notes section of link id 23973: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23973: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/PombertLab\/SYNY\" id=\"link-25700\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SYNY<\/a>\n<!-- Time to render name section of link id 25700: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The SYNY pipeline investigates gene collinearity (synteny) between genomes by reconstructing clusters from conserved pairs of protein-coding genes identified from DIAMOND homology searches. It also infers collinearity from pairwise genome alignments with minimap2 or MashMap3.<\/p>\n<!-- Time to render link large description section of link id 25700: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SYNY> How to use <\/a>\n<!-- Time to render notes section of link id 25700: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25700: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/www.tcoffee.org\/Projects\/tcoffee\" id=\"link-23745\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T-Coffee<\/a>\n<!-- Time to render name section of link id 23745: 1.9073486328125E-6 --> \n<\/td>\n<td><p>T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignmen.<\/p>\n<!-- Time to render link large description section of link id 23745: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_T-Coffee> How to use <\/a>\n<!-- Time to render notes section of link id 23745: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23745: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/tophat.cbcb.umd.edu\" id=\"link-23749\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tophat<\/a>\n<!-- Time to render name section of link id 23749: 2.1457672119141E-6 --> \n<\/td>\n<td><p>TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner <a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\/\" rel=\"nofollow\">Bowtie<\/a>, and then analyzes the mapping results to identify splice junctions between exons.<\/p>\n<!-- Time to render link large description section of link id 23749: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Tophat> How to use <\/a>\n<!-- Time to render notes section of link id 23749: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23749: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/www.gear-genomics.com\/docs\/tracy\/\" id=\"link-24568\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tracy<\/a>\n<!-- Time to render name section of link id 24568: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tracy is an efficient and versatile command-line application to basecall, align, assemble and deconvolute Sanger Chromatogram trace files.<\/p>\n<!-- Time to render link large description section of link id 24568: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24568: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24568: 0.0001068115234375 --> \n<tr><td><a href=\"http:\/\/trimal.cgenomics.org\/introduction\" id=\"link-23753\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">trimAl<\/a>\n<!-- Time to render name section of link id 23753: 2.1457672119141E-6 --> \n<\/td>\n<td><p>trimAl: a tool for automated alignment trimmin<\/p>\n<!-- Time to render link large description section of link id 23753: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_trimAl> How to use <\/a>\n<!-- Time to render notes section of link id 23753: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23753: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/ksahlin\/ultra\" id=\"link-24322\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">uLTRA<\/a>\n<!-- Time to render name section of link id 24322: 1.9073486328125E-6 --> \n<\/td>\n<td><p>uLTRA is a tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations.<\/p>\n<!-- Time to render link large description section of link id 24322: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_uLTRA> How to use <\/a>\n<!-- Time to render notes section of link id 24322: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24322: 0.00010895729064941 --> \n<tr><td><a href=\"http:\/\/www.drive5.com\/usearch\/\" id=\"link-23758\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">USEARCH<\/a>\n<!-- Time to render name section of link id 23758: 1.9073486328125E-6 --> \n<\/td>\n<td><p>USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.<\/p>\n<!-- Time to render link large description section of link id 23758: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_USEARCH> How to use <\/a>\n<!-- Time to render notes section of link id 23758: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23758: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/mskcc\/vcf2maf\" id=\"link-24577\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcf2maf<\/a>\n<!-- Time to render name section of link id 24577: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms.<\/p>\n<!-- Time to render link large description section of link id 24577: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcf2maf> How to use <\/a>\n<!-- Time to render notes section of link id 24577: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24577: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/vgteam\/vg\" id=\"link-24581\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vg<\/a>\n<!-- Time to render name section of link id 24581: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.<\/p>\n<!-- Time to render link large description section of link id 24581: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vg> How to use <\/a>\n<!-- Time to render notes section of link id 24581: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24581: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/torognes\/vsearch\" id=\"link-23787\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VSEARCH<\/a>\n<!-- Time to render name section of link id 23787: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Versatile open-source tool for metagenomics<\/p>\n<!-- Time to render link large description section of link id 23787: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VSEARCH> How to use <\/a>\n<!-- Time to render notes section of link id 23787: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23787: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/smarco\/WFA\" id=\"link-24588\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WFA<\/a>\n<!-- Time to render name section of link id 24588: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.<\/p>\n<!-- Time to render link large description section of link id 24588: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24588: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24588: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/waveygang\/wfmash\" id=\"link-24589\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wfmash<\/a>\n<!-- Time to render name section of link id 24589: 1.9073486328125E-6 --> \n<\/td>\n<td><p>wfmash is an aligner for pangenomes based on sparse homology mapping and wavefront inception.<\/p>\n<!-- Time to render link large description section of link id 24589: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24589: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24589: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/wjwei-handsome\/wgatools\" id=\"link-26098\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wgatools<\/a>\n<!-- Time to render name section of link id 26098: 6.9141387939453E-6 --> \n<\/td>\n<td><p>A Rust library and tools for whole genome alignment files.<\/p>\n<!-- Time to render link large description section of link id 26098: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_wgatools> How to use <\/a>\n<!-- Time to render notes section of link id 26098: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26098: 0.00053501129150391 --> \n<tr><td><a href=\"https:\/\/github.com\/SunPengChuan\/wgdi\" id=\"link-25319\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WGDI<\/a>\n<!-- Time to render name section of link id 25319: 6.1988830566406E-6 --> \n<\/td>\n<td>WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments.\n<!-- Time to render link large description section of link id 25319: 9.5367431640625E-7 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WGDI> How to use <\/a>\n<!-- Time to render notes section of link id 25319: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25319: 0.00034499168395996 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/Winnowmap\" id=\"link-24595\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Winnowmap<\/a>\n<!-- Time to render name section of link id 24595: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques.<\/p>\n<!-- Time to render link large description section of link id 24595: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24595: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24595: 0.00035309791564941 --> \n<tr><td><a href=\"https:\/\/www.advbiocomp.com\/blast\/obsolete\/\" id=\"link-23763\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">wu-blast<\/a>\n<!-- Time to render name section of link id 23763: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Similarity search against databanks, Washington University Blast.(OBSOLETE)<\/p>\n<!-- Time to render link large description section of link id 23763: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WuBlast> How to use <\/a>\n<!-- Time to render notes section of link id 23763: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23763: 0.00034785270690918 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1161\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            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Execution Time: 0.0021491050720215-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1161 level0\"><!-- Div Category --><div id=\"single-cell\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Single-cell<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/COMBINE-lab\/alevin-fry\" id=\"link-26094\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">alevin-fry<\/a>\n<!-- Time to render name section of link id 26094: 8.1062316894531E-6 --> \n<\/td>\n<td><p>alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.<\/p>\n<!-- Time to render link large description section of link id 26094: 2.1457672119141E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_alevin-fry> How to use <\/a>\n<!-- Time to render notes section of link id 26094: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26094: 0.0005490779876709 --> \n<tr><td><a href=\"https:\/\/github.com\/shimlab\/BLAZE\" id=\"link-25811\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BLAZE<\/a>\n<!-- Time to render name section of link id 25811: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Barcode identification from Long reads for AnalyZing single-cell gene Expression. SingleCell Nanopore sequencing data analysis.<\/p>\n<!-- Time to render link large description section of link id 25811: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BLAZE> How to use <\/a>\n<!-- Time to render notes section of link id 25811: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25811: 0.00034403800964355 --> \n<tr><td><a href=\"https:\/\/github.com\/broadinstitute\/CellBender\" id=\"link-24889\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CellBender<\/a>\n<!-- Time to render name section of link id 24889: 5.9604644775391E-6 --> \n<\/td>\n<td><p>CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.<\/p>\n<!-- Time to render link large description section of link id 24889: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CellBender> How to use <\/a>\n<!-- Time to render notes section of link id 24889: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24889: 0.00033402442932129 --> \n<tr><td><a href=\"https:\/\/github.com\/atarashansky\/SAMap\" id=\"link-25484\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SAMap<\/a>\n<!-- Time to render name section of link id 25484: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.<\/p>\n<!-- Time to render link large description section of link id 25484: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SAMap> How to use <\/a>\n<!-- Time to render notes section of link id 25484: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25484: 0.00033712387084961 --> \n<tr><td><a href=\"https:\/\/github.com\/scverse\/scanpy\" id=\"link-25104\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Scanpy<\/a>\n<!-- Time to render name section of link id 25104: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. \u00a0It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.<\/p>\n<!-- Time to render link large description section of link id 25104: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Scanpy> How to use <\/a>\n<!-- Time to render notes section of link id 25104: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25104: 0.00033712387084961 --> \n<tr><td><a href=\"https:\/\/github.com\/single-cell-genetics\/vireo\" id=\"link-25927\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vireoSNP<\/a>\n<!-- Time to render name section of link id 25927: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Vireo: Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.<\/p>\n<!-- Time to render link large description section of link id 25927: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vireoSNP> How to use <\/a>\n<!-- Time to render notes section of link id 25927: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25927: 0.00032806396484375 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1117\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        (\n            [title] => ASC\n        )\n\n)\n-->\n\n\n<!-- Link Results: WP_Query Object\n(\n    [query] => Array\n        (\n            [post_type] => link_library_links\n            [posts_per_page] => 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class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/gitlab.com\/psc_santos\/ACACIA\" id=\"link-25395\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ACACIA<\/a>\n<!-- Time to render name section of link id 25395: 6.9141387939453E-6 --> \n<\/td>\n<td><p>Allele CAlling proCedure for Illumina Amplicon sequencing data: This workflow aims at extracting allele information out of paired-end Illumina FASTQC files.<\/p>\n<!-- Time to render link large description section of link id 25395: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ACACIA> How to use <\/a>\n<!-- Time to render notes section of link id 25395: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25395: 0.0003659725189209 --> \n<tr><td><a href=\"https:\/\/github.com\/AdamaJava\/adamajava\" id=\"link-26021\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">AdamaJava<\/a>\n<!-- Time to render name section of link id 26021: 6.9141387939453E-6 --> \n<\/td>\n<td><p>The AdamaJava project holds code for variant callers and pipeline tools related to next-generation sequencing (NGS).<\/p>\n<!-- Time to render link large description section of link id 26021: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_AdamaJava> How to use <\/a>\n<!-- Time to render notes section of link id 26021: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26021: 0.00035405158996582 --> \n<tr><td><a href=\"http:\/\/adegenet.r-forge.r-project.org\" id=\"link-24134\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">adegenet<\/a>\n<!-- Time to render name section of link id 24134: 5.9604644775391E-6 --> \n<\/td>\n<td><p>R package dedicated to the exploratory analysis of genetic data. 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These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file. There are sequence data processing tools, diagnostic tools, and variant discovery tools, similar to GATK by the Broad Institute.<\/p>\n<!-- Time to render link large description section of link id 24313: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ATLAS> How to use <\/a>\n<!-- Time to render notes section of link id 24313: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24313: 0.0001518726348877 --> \n<tr><td><a href=\"https:\/\/github.com\/stevemussmann\/BayesAss3-SNPs\" id=\"link-24155\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BayesAss3-SNPs<\/a>\n<!-- Time to render name section of link id 24155: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Modification of BayesAss 3.0.4 to allow handling of large SNP datasets.<\/p>\n<!-- Time to render link large description section of link id 24155: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BayesAss3-SNPs> How to use <\/a>\n<!-- Time to render notes section of link id 24155: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24155: 0.0001518726348877 --> \n<tr><td><a href=\"https:\/\/samtools.github.io\/bcftools\/\" id=\"link-23880\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BCFtools<\/a>\n<!-- Time to render name section of link id 23880: 3.0994415283203E-6 --> \n<\/td>\n<td><p>utilities for variant calling and manipulating VCFs and BCFs.<\/p>\n<!-- Time to render link large description section of link id 23880: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Bcftools> How to use <\/a>\n<!-- Time to render notes section of link id 23880: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23880: 0.00014901161193848 --> \n<tr><td><a href=\"http:\/\/faculty.washington.edu\/browning\/beagle\/beagle.html\" id=\"link-23594\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Beagle<\/a>\n<!-- Time to render name section of link id 23594: 3.0994415283203E-6 --> \n<\/td>\n<td><p>BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.<\/p>\n<!-- Time to render link large description section of link id 23594: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Beagle> How to use <\/a>\n<!-- Time to render notes section of link id 23594: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23594: 0.0001518726348877 --> \n<tr><td><a href=\"https:\/\/github.com\/0xTCG\/biser\" id=\"link-25249\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BISER<\/a>\n<!-- Time to render name section of link id 25249: 4.0531158447266E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25249: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BISER> How to use <\/a>\n<!-- Time to render notes section of link id 25249: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25249: 0.00026607513427734 --> \n<tr><td><a href=\"https:\/\/github.com\/dnaase\/Bis-tools\" id=\"link-24161\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BisSNP<\/a>\n<!-- Time to render name section of link id 24161: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Accurate combined SNP\/Methylation calling.<\/p>\n<!-- Time to render link large description section of link id 24161: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24161: 2.1457672119141E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24161: 0.00022006034851074 --> \n<tr><td><a href=\"https:\/\/github.com\/genome\/breakdancer\" id=\"link-24036\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">BreakDancer<\/a>\n<!-- Time to render name section of link id 24036: 3.814697265625E-6 --> \n<\/td>\n<td><p>SV detection from paired end reads mapping.<\/p>\n<!-- Time to render link large description section of link id 24036: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_BreakDancer> How to use <\/a>\n<!-- Time to render notes section of link id 24036: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24036: 0.0001990795135498 --> \n<tr><td><a href=\"http:\/\/barricklab.org\/twiki\/bin\/view\/Lab\/ToolsBacterialGenomeResequencing\" id=\"link-23812\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">breseq<\/a>\n<!-- Time to render name section of link id 23812: 4.0531158447266E-6 --> \n<\/td>\n<td><p>breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.<\/p>\n<!-- Time to render link large description section of link id 23812: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_breseq> How to use <\/a>\n<!-- Time to render notes section of link id 23812: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23812: 0.0001981258392334 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/genomicepidemiology\/cgmlstfinder\" id=\"link-24174\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cgMLSTFinder<\/a>\n<!-- Time to render name section of link id 24174: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Core genome Multi-Locus Sequence Typing cgMLSTFinder runs KMA <1> against a chosen core genome MLST (cgMLST) database and outputs the detected alleles in a matrix file.<\/p>\n<!-- Time to render link large description section of link id 24174: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24174: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24174: 0.00022602081298828 --> \n<tr><td><a href=\"https:\/\/github.com\/HKU-BAL\/Clair3\" id=\"link-24181\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Clair3<\/a>\n<!-- Time to render name section of link id 24181: 3.814697265625E-6 --> \n<\/td>\n<td><p>Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.<\/p>\n<!-- Time to render link large description section of link id 24181: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Clair3> How to use <\/a>\n<!-- Time to render notes section of link id 24181: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24181: 0.00022387504577637 --> \n<tr><td><a href=\"https:\/\/github.com\/KCCG\/ClinSV\" id=\"link-25253\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ClinSV<\/a>\n<!-- Time to render name section of link id 25253: 4.0531158447266E-6 --> \n<\/td>\n<td>\n<!-- Time to render link large description section of link id 25253: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ClinSV> How to use <\/a>\n<!-- Time to render notes section of link id 25253: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25253: 0.00022983551025391 --> \n<tr><td><a href=\"https:\/\/ftp.sanger.ac.uk\/pub\/resources\/software\/cnd\/\" id=\"link-25314\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cnD<\/a>\n<!-- Time to render name section of link id 25314: 5.9604644775391E-6 --> \n<\/td>\n<td><p>cnD is a program to detect copy number variants from short-read sequence data.<\/p>\n<!-- Time to render link large description section of link id 25314: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cnD> How to use <\/a>\n<!-- Time to render notes section of link id 25314: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25314: 0.00019717216491699 --> \n<tr><td><a href=\"https:\/\/github.com\/etal\/cnvkit\" id=\"link-25090\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CNVkit<\/a>\n<!-- Time to render name section of link id 25090: 4.0531158447266E-6 --> \n<\/td>\n<td><p dir=\"auto\">A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.<\/p>\r\n<p dir=\"auto\">CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.<\/p>\r\n<p dir=\"auto\">Read the full documentation at:\u00a0<a href=\"http:\/\/cnvkit.readthedocs.io\/\" rel=\"nofollow\">http:\/\/cnvkit.readthedocs.io<\/a><\/p>\n<!-- Time to render link large description section of link id 25090: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CNVkit> How to use <\/a>\n<!-- Time to render notes section of link id 25090: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25090: 0.00019598007202148 --> \n<tr><td><a href=\"http:\/\/sv.gersteinlab.org\/\" id=\"link-23610\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CNVnator<\/a>\n<!-- Time to render name section of link id 23610: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A tool for CNV discovery and genotyping from depth of read mapping.<\/p>\n<!-- Time to render link large description section of link id 23610: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23610: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23610: 0.00019311904907227 --> \n<tr><td><a href=\"http:\/\/genoweb.toulouse.inra.fr\/~fcabanettes\/cnv\/cnvpipelines_genotoul.pdf\" id=\"link-23946\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Cnvpipelines<\/a>\n<!-- Time to render name section of link id 23946: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A pipeline to detect copy number variations (CNV) on several samples.<\/p>\n<!-- Time to render link large description section of link id 23946: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23946: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23946: 0.00020599365234375 --> \n<tr><td><a href=\"https:\/\/github.com\/jlapaijmans\/Consensify\" id=\"link-24185\" class=\"track_this_link \" rel=\"noopener noreferrer\">Consensify<\/a>\n<!-- Time to render name section of link id 24185: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to standard pseudohaploidisation.<\/p>\n<!-- Time to render link large description section of link id 24185: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24185: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24185: 0.00020813941955566 --> \n<tr><td><a href=\"https:\/\/github.com\/vibansal\/crisp\/\" id=\"link-24008\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CRISP<\/a>\n<!-- Time to render name section of link id 24008: 3.814697265625E-6 --> \n<\/td>\n<td><p>CRISP is a software program to detect SNPs and short indels from pooled sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24008: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24008: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24008: 0.00019001960754395 --> \n<tr><td><a href=\"https:\/\/github.com\/tjiangHIT\/cuteSV\" id=\"link-25187\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cuteSV<\/a>\n<!-- Time to render name section of link id 25187: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Long read based human genomic structural variation detection with cuteSV.<\/p>\n<!-- Time to render link large description section of link id 25187: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cuteSV> How to use <\/a>\n<!-- Time to render notes section of link id 25187: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25187: 0.00023388862609863 --> \n<tr><td><a href=\"https:\/\/github.com\/brentp\/cyvcf2\" id=\"link-26029\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">cyvcf2<\/a>\n<!-- Time to render name section of link id 26029: 4.0531158447266E-6 --> \n<\/td>\n<td><p>cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.<\/p>\n<!-- Time to render link large description section of link id 26029: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_cyvcf2> How to use <\/a>\n<!-- Time to render notes section of link id 26029: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26029: 0.00019693374633789 --> \n<tr><td><a href=\"https:\/\/github.com\/google\/deepvariant\" id=\"link-25349\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">DeepVariant<\/a>\n<!-- Time to render name section of link id 25349: 4.0531158447266E-6 --> \n<\/td>\n<td><p>DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.<\/p>\n<!-- Time to render link large description section of link id 25349: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_DeepVariant> How to use <\/a>\n<!-- Time to render notes section of link id 25349: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25349: 0.00019598007202148 --> \n<tr><td><a href=\"https:\/\/github.com\/dellytools\/delly\" id=\"link-23615\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Delly<\/a>\n<!-- Time to render name section of link id 23615: 4.0531158447266E-6 --> \n<\/td>\n<td><p>DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.<\/p>\n<!-- Time to render link large description section of link id 23615: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Delly> How to use <\/a>\n<!-- Time to render notes section of link id 23615: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23615: 0.00020790100097656 --> \n<tr><td><a href=\"https:\/\/github.com\/cstritt\/detettore\" id=\"link-24199\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">detettore<\/a>\n<!-- Time to render name section of link id 24199: 4.0531158447266E-6 --> \n<\/td>\n<td><p>A program to detect transposable element polymorphisms<\/p>\n<!-- Time to render link large description section of link id 24199: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24199: 5.0067901611328E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24199: 0.00020098686218262 --> \n<tr><td><a href=\"http:\/\/www.broadinstitute.org\/software\/discovar\/blog\/\" id=\"link-24201\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Discovar<\/a>\n<!-- Time to render name section of link id 24201: 3.814697265625E-6 --> \n<\/td>\n<td><p>Assemble genomes and find variants with DISCOVAR &amp; DISCOVAR\u00a0de\u00a0novo<\/p>\n<!-- Time to render link large description section of link id 24201: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24201: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24201: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/kcleal\/dysgu\" id=\"link-24205\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">dysgu<\/a>\n<!-- Time to render name section of link id 24205: 3.0994415283203E-6 --> \n<\/td>\n<td><p>dysgu-SV is a collection of tools for calling structural variants using short or long reads.<\/p>\n<!-- Time to render link large description section of link id 24205: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_dysgu> How to use <\/a>\n<!-- Time to render notes section of link id 24205: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24205: 0.00019407272338867 --> \n<tr><td><a href=\"https:\/\/github.com\/ExaScience\/elprep\" id=\"link-24210\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">elPrep<\/a>\n<!-- Time to render name section of link id 24210: 4.0531158447266E-6 --> \n<\/td>\n<td><p>elPrep is a high-performance tool for analyzing .sam\/.bam files (up to and including variant calling) in sequencing pipelines.<\/p>\n<!-- Time to render link large description section of link id 24210: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_elPrep> How to use <\/a>\n<!-- Time to render notes section of link id 24210: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24210: 0.00019288063049316 --> \n<tr><td><a href=\"https:\/\/github.com\/Ensembl\/ensembl-vep\" id=\"link-24213\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Ensembl-VEP<\/a>\n<!-- Time to render name section of link id 24213: 3.0994415283203E-6 --> \n<\/td>\n<td><p>VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.<\/p>\n<!-- Time to render link large description section of link id 24213: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Ensembl-VEP> How to use <\/a>\n<!-- Time to render notes section of link id 24213: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24213: 0.0001981258392334 --> \n<tr><td><a href=\"https:\/\/github.com\/EBIvariation\/eva-sub-cli\" id=\"link-26008\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">eva-sub-cli<\/a>\n<!-- Time to render name section of link id 26008: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The eva-sub-cli tool is a command line interface tool for data validation and upload.<\/p>\n<!-- Time to render link large description section of link id 26008: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_eva-sub-cli> How to use <\/a>\n<!-- Time to render notes section of link id 26008: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26008: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/github.com\/OATML\/EVE\" id=\"link-25330\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">EVE<\/a>\n<!-- Time to render name section of link id 25330: 3.0994415283203E-6 --> \n<\/td>\n<td><p>EVE is a set of protein-specific models providing for any single amino acid mutation of interest a score reflecting the propensity of the resulting protein to be pathogenic.<\/p>\n<!-- Time to render link large description section of link id 25330: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_EVE> How to use <\/a>\n<!-- Time to render notes section of link id 25330: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25330: 0.00011491775512695 --> \n<tr><td><a href=\"https:\/\/github.com\/LuyiTian\/FLAMES\" id=\"link-25920\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FLAMES<\/a>\n<!-- Time to render name section of link id 25920: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Full-length transcriptome splicing and mutation analysis.<\/p>\n<!-- Time to render link large description section of link id 25920: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_FLAMES> How to use <\/a>\n<!-- Time to render notes section of link id 25920: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25920: 0.00012707710266113 --> \n<tr><td><a href=\"https:\/\/github.com\/ekg\/freebayes\" id=\"link-23980\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">FreeBayes<\/a>\n<!-- Time to render name section of link id 23980: 3.0994415283203E-6 --> \n<\/td>\n<td><p>FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.<\/p>\n<!-- Time to render link large description section of link id 23980: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_freebayes> How to use <\/a>\n<!-- Time to render notes section of link id 23980: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23980: 0.00014615058898926 --> \n<tr><td><a href=\"http:\/\/www.broadinstitute.org\/gsa\/wiki\/index.php\/The_Genome_Analysis_Toolkit\" id=\"link-23634\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GATK<\/a>\n<!-- Time to render name section of link id 23634: 2.8610229492188E-6 --> \n<\/td>\n<td><p>The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP\/indel caller and a local realigner.<\/p>\n<!-- Time to render link large description section of link id 23634: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GATK> How to use <\/a>\n<!-- Time to render notes section of link id 23634: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23634: 0.00013518333435059 --> \n<tr><td><a href=\"https:\/\/github.com\/heathsc\/gemBS-rs\" id=\"link-24243\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gemBS<\/a>\n<!-- Time to render name section of link id 24243: 2.8610229492188E-6 --> \n<\/td>\n<td><p>gemBS is a high performance bioinformatic pipeline designed for highthroughput analysis of DNA methylation data from whole genome bisulfites sequencing data (WGBS). It combines GEM3, a high performance read aligner and bs_call, a high performance variant and methyation caller, into a streamlined and efficient pipeline for bisulfite sequence analysis.<\/p>\n<!-- Time to render link large description section of link id 24243: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gemBS> How to use <\/a>\n<!-- Time to render notes section of link id 24243: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24243: 0.00013399124145508 --> \n<tr><td><a href=\"http:\/\/software.broadinstitute.org\/software\/genomestrip\/\" id=\"link-23817\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GenomeSTRiP<\/a>\n<!-- Time to render name section of link id 23817: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.<\/p>\n<!-- Time to render link large description section of link id 23817: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23817: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23817: 0.0001370906829834 --> \n<tr><td><a href=\"https:\/\/github.com\/DRL\/gIMble\" id=\"link-24102\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gIMble<\/a>\n<!-- Time to render name section of link id 24102: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A genome-wide IM blockwise likelihood estimation toolkit<\/p>\n<!-- Time to render link large description section of link id 24102: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24102: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24102: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/graphtyper\" id=\"link-24263\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">graphtyper<\/a>\n<!-- Time to render name section of link id 24263: 3.0994415283203E-6 --> \n<\/td>\n<td><p>graphtyper is a graph-based variant caller capable of genotyping population-scale short read data sets.<\/p>\n<!-- Time to render link large description section of link id 24263: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_graphtyper> How to use <\/a>\n<!-- Time to render notes section of link id 24263: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24263: 0.00014996528625488 --> \n<tr><td><a href=\"https:\/\/github.com\/PapenfussLab\/gridss\" id=\"link-24264\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GRIDSS<\/a>\n<!-- Time to render name section of link id 24264: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.<\/p>\n<!-- Time to render link large description section of link id 24264: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GRIDSS> How to use <\/a>\n<!-- Time to render notes section of link id 24264: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24264: 0.00013518333435059 --> \n<tr><td><a href=\"http:\/\/www.well.ox.ac.uk\/~cfreeman\/software\/gwas\/gtool.html\" id=\"link-23792\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Gtools<\/a>\n<!-- Time to render name section of link id 23792: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.<\/p>\n<!-- Time to render link large description section of link id 23792: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23792: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23792: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/vibansal\/HapCUT2\" id=\"link-23841\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HapCUT2<\/a>\n<!-- Time to render name section of link id 23841: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Software tools for haplotype assembly from sequence data<\/p>\n<!-- Time to render link large description section of link id 23841: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HapCUT2> How to use <\/a>\n<!-- Time to render notes section of link id 23841: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23841: 0.00013399124145508 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/harvest-tools\" id=\"link-25350\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HarvestTools<\/a>\n<!-- Time to render name section of link id 25350: 1.9073486328125E-6 --> \n<\/td>\n<td><p>HarvestTools is a utility for creating and interfacing with Gingr files, which are efficient archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.<\/p>\n<!-- Time to render link large description section of link id 25350: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HarvestTools> How to use <\/a>\n<!-- Time to render notes section of link id 25350: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25350: 0.0001380443572998 --> \n<tr><td><a href=\"https:\/\/github.com\/qiyunlab\/HGTector\" id=\"link-24285\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HGTector<\/a>\n<!-- Time to render name section of link id 24285: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.<\/p>\n<!-- Time to render link large description section of link id 24285: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24285: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24285: 0.00013494491577148 --> \n<tr><td><a href=\"https:\/\/github.com\/mkirsche\/Iris\" id=\"link-25321\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Iris<\/a>\n<!-- Time to render name section of link id 25321: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A module which corrects the sequences of structural variant calls (currently only insertions).<\/p>\n<!-- Time to render link large description section of link id 25321: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Iris> How to use <\/a>\n<!-- Time to render notes section of link id 25321: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25321: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/wonder.cdc.gov\/amd\/flu\/irma\/\" id=\"link-24325\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">IRMA<\/a>\n<!-- Time to render name section of link id 24325: 3.0994415283203E-6 --> \n<\/td>\n<td><p>IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza and ebolavirus. IRMA is free to use and parallelizes computations for both cluster computing and single computer multi-core setups.<\/p>\n<!-- Time to render link large description section of link id 24325: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_IRMA> How to use <\/a>\n<!-- Time to render notes section of link id 24325: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24325: 0.00013184547424316 --> \n<tr><td><a href=\"https:\/\/github.com\/andersen-lab\/ivar\" id=\"link-25121\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iVar<\/a>\n<!-- Time to render name section of link id 25121: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Var is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions\/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.<\/p>\n<!-- Time to render link large description section of link id 25121: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_iVar> How to use <\/a>\n<!-- Time to render notes section of link id 25121: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25121: 0.00013613700866699 --> \n<tr><td><a href=\"https:\/\/github.com\/mkirsche\/Jasmine\" id=\"link-25042\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jasmine<\/a>\n<!-- Time to render name section of link id 25042: 2.1457672119141E-6 --> \n<\/td>\n<td><p dir=\"auto\">JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges. This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.<\/p>\r\n<p dir=\"auto\">Manual : <a href=\"https:\/\/github.com\/mkirsche\/Jasmine\/wiki\/Jasmine-User-Manual\">Jasmine User Manual \u00b7 mkirsche\/Jasmine Wiki \u00b7 GitHub<\/a><\/p>\r\n<p dir=\"auto\">Jasmine also includes a module for automating the creation of\u00a0<a href=\"http:\/\/software.broadinstitute.org\/software\/igv\/\" rel=\"nofollow\">IGV<\/a>\u00a0screenshots of variants of interest.<\/p>\n<!-- Time to render link large description section of link id 25042: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Jasmine> How to use <\/a>\n<!-- Time to render notes section of link id 25042: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25042: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/lindenb\/jvarkit\" id=\"link-24334\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jvarkit<\/a>\n<!-- Time to render name section of link id 24334: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Java utilities for Bioinformatics (only requested tools are compiling)<\/p>\n<!-- Time to render link large description section of link id 24334: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24334: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24334: 0.00013899803161621 --> \n<tr><td><a href=\"https:\/\/www.kingrelatedness.com\" id=\"link-24336\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">KING<\/a>\n<!-- Time to render name section of link id 24336: 3.0994415283203E-6 --> \n<\/td>\n<td><p>KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project.<\/p>\n<!-- Time to render link large description section of link id 24336: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_KING> How to use <\/a>\n<!-- Time to render notes section of link id 24336: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24336: 0.00014305114746094 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/ksnp\/\" id=\"link-25283\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">kSNP4<\/a>\n<!-- Time to render name section of link id 25283: 3.0994415283203E-6 --> \n<\/td>\n<td><p>kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.<\/p>\n<!-- Time to render link large description section of link id 25283: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_kSNP4> How to use <\/a>\n<!-- Time to render notes section of link id 25283: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25283: 0.00014495849609375 --> \n<tr><td><a href=\"https:\/\/github.com\/sudmantlab\/loco-pipe\" id=\"link-25804\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">loco-pipe<\/a>\n<!-- Time to render name section of link id 25804: 2.8610229492188E-6 --> \n<\/td>\n<td><p>loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data.<\/p>\n<!-- Time to render link large description section of link id 25804: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_loco-pipe> How to use <\/a>\n<!-- Time to render notes section of link id 25804: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25804: 0.00013518333435059 --> \n<tr><td><a href=\"https:\/\/github.com\/CSB5\/lofreq\" id=\"link-24353\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LoFreq<\/a>\n<!-- Time to render name section of link id 24353: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A sequence-quality aware, ultra-sensitive variant caller for NGS data.<\/p>\n<!-- Time to render link large description section of link id 24353: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LoFreq> How to use <\/a>\n<!-- Time to render notes section of link id 24353: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24353: 0.0001370906829834 --> \n<tr><td><a href=\"https:\/\/support.10xgenomics.com\/genome-exome\/software\/pipelines\/latest\/what-is-long-ranger\" id=\"link-23879\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LongRanger<\/a>\n<!-- Time to render name section of link id 23879: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.<\/p>\n<!-- Time to render link large description section of link id 23879: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LongRanger> How to use <\/a>\n<!-- Time to render notes section of link id 23879: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23879: 0.00013613700866699 --> \n<tr><td><a href=\"https:\/\/github.com\/pjedge\/longshot\" id=\"link-24355\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">longshot<\/a>\n<!-- Time to render name section of link id 24355: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).<\/p>\n<!-- Time to render link large description section of link id 24355: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24355: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24355: 0.00013303756713867 --> \n<tr><td><a href=\"https:\/\/github.com\/arq5x\/lumpy-sv\" id=\"link-23918\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">LUMPY<\/a>\n<!-- Time to render name section of link id 23918: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A general probabilistic framework for structural variant discovery<\/p>\n<!-- Time to render link large description section of link id 23918: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_LUMPY> How to use <\/a>\n<!-- Time to render notes section of link id 23918: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 23918: 0.00014305114746094 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/manta\" id=\"link-24364\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Manta<\/a>\n<!-- Time to render name section of link id 24364: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.<\/p>\n<!-- Time to render link large description section of link id 24364: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Manta> How to use <\/a>\n<!-- Time to render notes section of link id 24364: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24364: 0.00014185905456543 --> \n<tr><td><a href=\"https:\/\/www.staff.ncl.ac.uk\/richard.howey\/mapthin\/\" id=\"link-24365\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MapThin<\/a>\n<!-- Time to render name section of link id 24365: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Reduce the number of SNPs in a gene marker dense map computed by PLINK. First, by eliminating linked SNPs. Then, by applying different criteria.<\/p>\n<!-- Time to render link large description section of link id 24365: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24365: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24365: 0.00017690658569336 --> \n<tr><td><a href=\"https:\/\/github.com\/arangrhie\/merfin\" id=\"link-24371\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Merfin<\/a>\n<!-- Time to render name section of link id 24371: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Evaluate variant calls and its combination with k-mer multiplicity.<\/p>\n<!-- Time to render link large description section of link id 24371: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24371: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24371: 0.00011301040649414 --> \n<tr><td><a href=\"https:\/\/github.com\/KCCG\/mity\" id=\"link-25760\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">mity<\/a>\n<!-- Time to render name section of link id 25760: 1.9073486328125E-6 --> \n<\/td>\n<td>A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data \n<!-- Time to render link large description section of link id 25760: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_mity> How to use <\/a>\n<!-- Time to render notes section of link id 25760: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25760: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/jyhehir\/mobster\" id=\"link-23669\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Mobster<\/a>\n<!-- Time to render name section of link id 23669: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Mobster is used to detect novel (non-reference) Mobile Element Insertion (MEI) events in BAM files and uses both a discordant read pair method and a split-read method.<\/p>\n<!-- Time to render link large description section of link id 23669: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23669: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23669: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/WGLab\/NanoCaller\" id=\"link-24406\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">NanoCaller<\/a>\n<!-- Time to render name section of link id 24406: 1.9073486328125E-6 --> \n<\/td>\n<td><p>NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs\/indels from long-read sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24406: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_NanoCaller> How to use <\/a>\n<!-- Time to render notes section of link id 24406: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24406: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/MikkelSchubert\/paleomix\/wiki\/Overview\" id=\"link-23684\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PALEOMIX<\/a>\n<!-- Time to render name section of link id 23684: 3.0994415283203E-6 --> \n<\/td>\n<td><p>The PALEOMIX pipeline is a set of free and open-source pipelines and tools designed to enable the rapid processing of Next Generation Sequencing (NGS) data, starting from de-multiplexed reads from one or more samples, through sequence processing and alignment, and ending with genotyping, phylogenetic inference on the samples, as well as metagenomic analysis of the samples.<\/p>\n<!-- Time to render link large description section of link id 23684: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PALEOMIX> How to use <\/a>\n<!-- Time to render notes section of link id 23684: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23684: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/eblerjana\/pangenie\" id=\"link-24960\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PanGenie<\/a>\n<!-- Time to render name section of link id 24960: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph.<\/p>\n<!-- Time to render link large description section of link id 24960: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PanGenie> How to use <\/a>\n<!-- Time to render notes section of link id 24960: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24960: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/paragraph\" id=\"link-24430\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Paragraph<\/a>\n<!-- Time to render name section of link id 24430: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Graph realignment tools for structural variants.<\/p>\n<!-- Time to render link large description section of link id 24430: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Paragraph> How to use <\/a>\n<!-- Time to render notes section of link id 24430: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24430: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/parsnp\" id=\"link-24971\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Parsnp<\/a>\n<!-- Time to render name section of link id 24971: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.<\/p>\n<!-- Time to render link large description section of link id 24971: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Parsnp> How to use <\/a>\n<!-- Time to render notes section of link id 24971: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24971: 0.00011706352233887 --> \n<tr><td><a href=\"https:\/\/github.com\/Rosemeis\/pcangsd\" id=\"link-24019\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PCAngsd<\/a>\n<!-- Time to render name section of link id 24019: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Framework for analyzing low depth next-generation sequencing (NGS) data in heterogeneous populations using principal component analysis (PCA).<\/p>\n<!-- Time to render link large description section of link id 24019: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PCAngsd> How to use <\/a>\n<!-- Time to render notes section of link id 24019: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24019: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/pangenome\/pggb\" id=\"link-24887\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">pggb<\/a>\n<!-- Time to render name section of link id 24887: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pangenome graph builder.<\/p>\n<!-- Time to render link large description section of link id 24887: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_pggb> How to use <\/a>\n<!-- Time to render notes section of link id 24887: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24887: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/broadinstitute\/pilon\" id=\"link-23821\" class=\"track_this_link \" rel=\"noopener noreferrer\">Pilon<\/a>\n<!-- Time to render name section of link id 23821: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Pilon is an automated genome assembly improvement and variant detection tool.<\/p>\n<!-- Time to render link large description section of link id 23821: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pilon> How to use <\/a>\n<!-- Time to render notes section of link id 23821: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23821: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/gmt.genome.wustl.edu\/packages\/pindel\/index.html\" id=\"link-23696\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Pindel<\/a>\n<!-- Time to render name section of link id 23696: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.<\/p>\n<!-- Time to render link large description section of link id 23696: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Pindel> How to use <\/a>\n<!-- Time to render notes section of link id 23696: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23696: 0.00014305114746094 --> \n<tr><td><a href=\"https:\/\/github.com\/diriano\/ploidyNGS\" id=\"link-24081\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ploidyNGS<\/a>\n<!-- Time to render name section of link id 24081: 3.0994415283203E-6 --> \n<\/td>\n<td><p>A model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data.<\/p>\n<!-- Time to render link large description section of link id 24081: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24081: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24081: 0.00015401840209961 --> \n<tr><td><a href=\"https:\/\/github.com\/bkehr\/popins\" id=\"link-23849\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">popins<\/a>\n<!-- Time to render name section of link id 23849: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Population-scale detection of novel-sequence insertions.<\/p>\n<!-- Time to render link large description section of link id 23849: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23849: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23849: 0.00011420249938965 --> \n<tr><td><a href=\"https:\/\/github.com\/kehrlab\/PopIns2\" id=\"link-24998\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PopIns2<\/a>\n<!-- Time to render name section of link id 24998: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs.<\/p>\n<!-- Time to render link large description section of link id 24998: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24998: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24998: 0.00012516975402832 --> \n<tr><td><a href=\"https:\/\/github.com\/alachins\/raisd\" id=\"link-24482\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RAiSD<\/a>\n<!-- Time to render name section of link id 24482: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RAiSD (Raised Accuracy in Sweep Detection) is a stand-alone software implementation of the \u03bc statistic for selective sweep detection.<\/p>\n<!-- Time to render link large description section of link id 24482: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RAiSD> How to use <\/a>\n<!-- Time to render notes section of link id 24482: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24482: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/rdxplorer.sourceforge.net\/\" id=\"link-25313\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RDXplorer<\/a>\n<!-- Time to render name section of link id 25313: 2.1457672119141E-6 --> \n<\/td>\n<td><p>The RDXplorer (Read Depth eXplorer) is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.<\/p>\n<!-- Time to render link large description section of link id 25313: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RDXplorer> How to use <\/a>\n<!-- Time to render notes section of link id 25313: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25313: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/cpouchon\/REFMAKER\" id=\"link-25264\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REFMAKER<\/a>\n<!-- Time to render name section of link id 25264: 1.9073486328125E-6 --> \n<\/td>\n<td><p>REFMAKER is a command-line and user-friendly pipeline providing different tools to create nuclear references from genomic assemblies of shotgun libraries.<\/p>\n<!-- Time to render link large description section of link id 25264: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REFMAKER> How to use <\/a>\n<!-- Time to render notes section of link id 25264: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25264: 0.00011992454528809 --> \n<tr><td><a href=\"https:\/\/github.com\/griffithlab\/regtools\" id=\"link-24487\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RegTools<\/a>\n<!-- Time to render name section of link id 24487: 2.1457672119141E-6 --> \n<\/td>\n<td><p>RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.<\/p>\n<!-- Time to render link large description section of link id 24487: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24487: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24487: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/grenaud\/ROHan\" id=\"link-24503\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">ROHan<\/a>\n<!-- Time to render name section of link id 24503: 2.1457672119141E-6 --> \n<\/td>\n<td><p>ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity.<\/p>\n<!-- Time to render link large description section of link id 24503: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_ROHan> How to use <\/a>\n<!-- Time to render notes section of link id 24503: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24503: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/RealTimeGenomics\/rtg-tools\" id=\"link-26164\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">RTGTools<\/a>\n<!-- Time to render name section of link id 26164: 1.9073486328125E-6 --> \n<\/td>\n<td><p>RTG Tools is a subset of\u00a0<a href=\"https:\/\/github.com\/RealTimeGenomics\/rtg-core\">RTG Core<\/a>\u00a0that includes several useful utilities for dealing with VCF files and sequence data. Probably the most interesting is the\u00a0<code>vcfeval<\/code>\u00a0command which performs sophisticated comparison of VCF files.<\/p>\n<!-- Time to render link large description section of link id 26164: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_RTGTools> How to use <\/a>\n<!-- Time to render notes section of link id 26164: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26164: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/vpc-ccg\/sedef\" id=\"link-24028\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SEDEF<\/a>\n<!-- Time to render name section of link id 24028: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SEDEF is a quick tool to find all segmental duplications in the genome.<\/p>\n<!-- Time to render link large description section of link id 24028: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24028: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24028: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/stschiff\/sequenceTools\" id=\"link-24078\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SequenceTools<\/a>\n<!-- Time to render name section of link id 24078: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Tools for population genetics on sequencing datas<\/p>\n<!-- Time to render link large description section of link id 24078: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SequenceTools> How to use <\/a>\n<!-- Time to render notes section of link id 24078: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24078: 0.00012516975402832 --> \n<tr><td><a href=\"https:\/\/mathgen.stats.ox.ac.uk\/genetics_software\/shapeit\/shapeit.html#home\" id=\"link-23771\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SHAPEIT<\/a>\n<!-- Time to render name section of link id 23771: 3.0994415283203E-6 --> \n<\/td>\n<td><p>SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.<\/p>\n<!-- Time to render link large description section of link id 23771: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SHAPEIT> How to use <\/a>\n<!-- Time to render notes section of link id 23771: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23771: 0.00012302398681641 --> \n<tr><td><a href=\"https:\/\/github.com\/rvaser\/sift4g\" id=\"link-24723\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SIFT4G<\/a>\n<!-- Time to render name section of link id 24723: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Sorting Intolerant From Tolerant For Genomes.<\/p>\n<!-- Time to render link large description section of link id 24723: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SIFT4G> How to use <\/a>\n<!-- Time to render notes section of link id 24723: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24723: 0.00012803077697754 --> \n<tr><td><a href=\"https:\/\/github.com\/pauline-ng\/SIFT4G_Annotator\" id=\"link-24724\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SIFT4G_Annotator<\/a>\n<!-- Time to render name section of link id 24724: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Annotating VCF files using the SIFT4G databases.<\/p>\n<!-- Time to render link large description section of link id 24724: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24724: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24724: 0.00010991096496582 --> \n<tr><td><a href=\"https:\/\/code.google.com\/archive\/p\/snape-pooled\/\" id=\"link-24089\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snape-pooled<\/a>\n<!-- Time to render name section of link id 24089: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.<\/p>\n<!-- Time to render link large description section of link id 24089: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24089: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24089: 0.00010085105895996 --> \n<tr><td><a href=\"https:\/\/github.com\/fritzsedlazeck\/Sniffles\" id=\"link-24524\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Sniffles<\/a>\n<!-- Time to render name section of link id 24524: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.<\/p>\n<!-- Time to render link large description section of link id 24524: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Sniffles> How to use <\/a>\n<!-- Time to render notes section of link id 24524: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24524: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/tseemann\/snippy\" id=\"link-24075\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Snippy<\/a>\n<!-- Time to render name section of link id 24075: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Rapid haploid variant calling and core genome alignment. Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions\/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree).<\/p>\n<!-- Time to render link large description section of link id 24075: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Snippy> How to use <\/a>\n<!-- Time to render notes section of link id 24075: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24075: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-pathogens\/snp-sites\" id=\"link-24861\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNP-sites<\/a>\n<!-- Time to render name section of link id 24861: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Rapidly extracts SNPs from a multi-FASTA alignment.<\/p>\n<!-- Time to render link large description section of link id 24861: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNP-sites> How to use <\/a>\n<!-- Time to render notes section of link id 24861: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24861: 0.00010108947753906 --> \n<tr><td><a href=\"https:\/\/github.com\/harvardinformatics\/snpArcher\" id=\"link-25580\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">snpArcher<\/a>\n<!-- Time to render name section of link id 25580: 1.9073486328125E-6 --> \n<\/td>\n<td><p>snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakemake workflow management system, for dataset acquisition, variant calling, quality control, and downstream analysis.<\/p>\n<!-- Time to render link large description section of link id 25580: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_snpArcher> How to use <\/a>\n<!-- Time to render notes section of link id 25580: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25580: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/pcingola.github.io\/SnpEff\/\" id=\"link-23732\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SnpEff<\/a>\n<!-- Time to render name section of link id 23732: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SnpEff is a variant annotation and effect prediction tool. ttttIt annotates and predicts the effects of variants on genes (such as amino acid changes)<\/p>\n<!-- Time to render link large description section of link id 23732: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SnpEff> How to use <\/a>\n<!-- Time to render notes section of link id 23732: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23732: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/chasewnelson\/SNPGenie\" id=\"link-24525\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPGenie<\/a>\n<!-- Time to render name section of link id 24525: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SNPGenie is a collection of Perl scripts for estimating \u03c0N\/\u03c0S, dN\/dS, and gene diversity from next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data.<\/p>\n<!-- Time to render link large description section of link id 24525: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24525: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24525: 0.0001070499420166 --> \n<tr><td><a href=\"http:\/\/chibba.pgml.uga.edu\/snphylo\" id=\"link-23795\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPhylo<\/a>\n<!-- Time to render name section of link id 23795: 1.9073486328125E-6 --> \n<\/td>\n<td><p>a pipeline to generate a phylogenetic tree from huge SNP data<\/p>\n<!-- Time to render link large description section of link id 23795: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNPhylo> How to use <\/a>\n<!-- Time to render notes section of link id 23795: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23795: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/FelixKrueger\/SNPsplit\" id=\"link-25013\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SNPsplit<\/a>\n<!-- Time to render name section of link id 25013: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SNPsplit is an allele-specific alignment sorter which is designed to read alignment files in SAM\/BAM format and determine the allelic origin of reads that cover known SNP positions.<\/p>\n<!-- Time to render link large description section of link id 25013: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SNPsplit> How to use <\/a>\n<!-- Time to render notes section of link id 25013: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25013: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/hall-lab\/speedseq\" id=\"link-24128\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SpeedSeq<\/a>\n<!-- Time to render name section of link id 24128: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A flexible framework for rapid genome analysis and interpretation.<\/p>\n<!-- Time to render link large description section of link id 24128: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24128: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24128: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/STAR-Fusion\/STAR-Fusion\" id=\"link-23740\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">STAR-Fusion<\/a>\n<!-- Time to render name section of link id 23740: 1.9073486328125E-6 --> \n<\/td>\n<td><p>STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set (using a GTF file, ideally the same annotation file used during the STAR genome index building process during the intial STAR setup).<\/p>\n<!-- Time to render link large description section of link id 23740: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_STAR-Fusion> How to use <\/a>\n<!-- Time to render notes section of link id 23740: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23740: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/strelka\" id=\"link-23984\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Strelka<\/a>\n<!-- Time to render name section of link id 23984: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor\/normal sample pairs.<\/p>\n<!-- Time to render link large description section of link id 23984: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Strelka> How to use <\/a>\n<!-- Time to render notes section of link id 23984: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23984: 0.00010800361633301 --> \n<tr><td><a href=\"http:\/\/bioinf.wehi.edu.au\/subread-package\/\" id=\"link-23743\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Subread<\/a>\n<!-- Time to render name section of link id 23743: 2.1457672119141E-6 --> \n<\/td>\n<td><p>A tool kit for processing next-gen sequencing data<\/p>\n<!-- Time to render link large description section of link id 23743: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Subread> How to use <\/a>\n<!-- Time to render notes section of link id 23743: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 23743: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/fritzsedlazeck\/SURVIVOR\" id=\"link-24017\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SURVIVOR<\/a>\n<!-- Time to render name section of link id 24017: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SURVIVOR is a tool set for simulating\/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.<\/p>\n<!-- Time to render link large description section of link id 24017: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SURVIVOR> How to use <\/a>\n<!-- Time to render notes section of link id 24017: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24017: 0.00010085105895996 --> \n<tr><td><a href=\"https:\/\/github.com\/walaj\/svaba\" id=\"link-24095\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SvABA<\/a>\n<!-- Time to render name section of link id 24095: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Structural variation and indel detection by local assembly<\/p>\n<!-- Time to render link large description section of link id 24095: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SvABA> How to use <\/a>\n<!-- Time to render notes section of link id 24095: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24095: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/nhansen\/SVanalyzer\" id=\"link-24550\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVanalyzer<\/a>\n<!-- Time to render name section of link id 24550: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tools for the analysis of structural variation in genomes.<\/p>\n<!-- Time to render link large description section of link id 24550: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24550: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24550: 9.7036361694336E-5 --> \n<tr><td><a href=\"http:\/\/svdetect.sourceforge.net\/Site\/Home.html\" id=\"link-24014\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVDetect<\/a>\n<!-- Time to render name section of link id 24014: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.<\/p>\n<!-- Time to render link large description section of link id 24014: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24014: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24014: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/eldariont\/svim\" id=\"link-24103\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVIM<\/a>\n<!-- Time to render name section of link id 24103: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SVIM is a structural variant caller for long reads. It is able to detect, classify and genotype five different classes of structural variants.<\/p>\n<!-- Time to render link large description section of link id 24103: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVIM> How to use <\/a>\n<!-- Time to render notes section of link id 24103: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24103: 9.918212890625E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/eldariont\/svim-asm\" id=\"link-24857\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVIM-asm<\/a>\n<!-- Time to render name section of link id 24857: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SVIM-asm (pronounced SWIM-assem) is a structural variant caller for haploid or diploid genome-genome alignments.<\/p>\n<!-- Time to render link large description section of link id 24857: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVIM-asm> How to use <\/a>\n<!-- Time to render notes section of link id 24857: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24857: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/DecodeGenetics\/svimmer\" id=\"link-24551\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">svimmer<\/a>\n<!-- Time to render name section of link id 24551: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Merges similar SVs from multiple single sample VCF files. The tool was written for merging SVs discovered using Manta calls, but should support (almost) any SV VCFs.<\/p>\n<!-- Time to render link large description section of link id 24551: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24551: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24551: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/llecompte\/SVJedi\" id=\"link-24552\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi<\/a>\n<!-- Time to render name section of link id 24552: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SVJedi is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24552: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24552: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24552: 0.00011610984802246 --> \n<tr><td><a href=\"https:\/\/github.com\/SandraLouise\/SVJedi-graph\" id=\"link-24752\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVJedi-graph<\/a>\n<!-- Time to render name section of link id 24752: 2.1457672119141E-6 --> \n<\/td>\n<td><p>SVJedi-graph is a structural variation (SV) genotyper for long read data.<\/p>\n<!-- Time to render link large description section of link id 24752: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVJedi-graph> How to use <\/a>\n<!-- Time to render notes section of link id 24752: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24752: 0.00011897087097168 --> \n<tr><td><a href=\"https:\/\/svmerge.sourceforge.net\/\" id=\"link-25315\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SVMerge<\/a>\n<!-- Time to render name section of link id 25315: 2.8610229492188E-6 --> \n<\/td>\n<td><p>A pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly.<\/p>\n<!-- Time to render link large description section of link id 25315: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVMerge> How to use <\/a>\n<!-- Time to render notes section of link id 25315: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25315: 0.00012111663818359 --> \n<tr><td><a href=\"https:\/\/github.com\/hall-lab\/svtyper\" id=\"link-23832\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">svtyper<\/a>\n<!-- Time to render name section of link id 23832: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Bayesian genotyper for structural variants.<\/p>\n<!-- Time to render link large description section of link id 23832: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SVTyper> How to use <\/a>\n<!-- Time to render notes section of link id 23832: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23832: 0.00011801719665527 --> \n<tr><td><a href=\"https:\/\/schneebergerlab.github.io\/syri\/\" id=\"link-24554\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">SyRI<\/a>\n<!-- Time to render name section of link id 24554: 1.9073486328125E-6 --> \n<\/td>\n<td><p>SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA).<\/p>\n<!-- Time to render link large description section of link id 24554: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_SyRI> How to use <\/a>\n<!-- Time to render notes section of link id 24554: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24554: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/mourisl\/T1K\" id=\"link-26025\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">T1K<\/a>\n<!-- Time to render name section of link id 26025: 2.1457672119141E-6 --> \n<\/td>\n<td><p>T1K (The ONE genotyper for Kir and HLA) is a computational tool to infer the alleles for the polymorphic genes such as KIR and HLA. T1K calculates the allele abundances based on the RNA-seq\/WES\/WGS read alignments on the provided allele reference sequences. The abundances are used to pick the true alleles for each gene. T1K provides the post analysis steps, including novel SNP detection and single-cell representation. T1K supports both single-end and paired-end sequencing data with any read length.<\/p>\n<!-- Time to render link large description section of link id 26025: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_T1K> How to use <\/a>\n<!-- Time to render notes section of link id 26025: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26025: 9.9897384643555E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/BilkentCompGen\/tardis\" id=\"link-24851\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TARDIS<\/a>\n<!-- Time to render name section of link id 24851: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Toolkit for automated and rapid discovery of structural variants.<\/p>\n<!-- Time to render link large description section of link id 24851: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24851: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24851: 9.8943710327148E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/cmdcolin\/TEnest\" id=\"link-25488\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TEnest<\/a>\n<!-- Time to render name section of link id 25488: 1.9073486328125E-6 --> \n<\/td>\n<td><p>TEnest is a tool for finding and annotating transposable element (TE) insertions.<\/p>\n<!-- Time to render link large description section of link id 25488: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TEnest> How to use <\/a>\n<!-- Time to render notes section of link id 25488: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25488: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/www.gear-genomics.com\/docs\/tracy\/\" id=\"link-24568\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Tracy<\/a>\n<!-- Time to render name section of link id 24568: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Tracy is an efficient and versatile command-line application to basecall, align, assemble and deconvolute Sanger Chromatogram trace files.<\/p>\n<!-- Time to render link large description section of link id 24568: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24568: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24568: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/spiralgenetics\/truvari\" id=\"link-24056\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Truvari<\/a>\n<!-- Time to render name section of link id 24056: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Structural variant comparison tool for VCFs<\/p>\n<!-- Time to render link large description section of link id 24056: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Truvari> How to use <\/a>\n<!-- Time to render notes section of link id 24056: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24056: 0.0001068115234375 --> \n<tr><td><a href=\"https:\/\/github.com\/AstraZeneca-NGS\/VarDict\" id=\"link-24574\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VarDict<\/a>\n<!-- Time to render name section of link id 24574: 2.1457672119141E-6 --> \n<\/td>\n<td><p>VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files.<\/p>\n<!-- Time to render link large description section of link id 24574: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24574: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24574: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/gitlab.com\/treangenlab\/variabel\" id=\"link-24575\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Variabel<\/a>\n<!-- Time to render name section of link id 24575: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A novel approach and method for intrahost variant detection, which outperforms existing ONT variant callers.<\/p>\n<!-- Time to render link large description section of link id 24575: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24575: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24575: 0.00010919570922852 --> \n<tr><td><a href=\"http:\/\/varscan.sourceforge.net\/\" id=\"link-23759\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VarScan<\/a>\n<!-- Time to render name section of link id 23759: 1.9073486328125E-6 --> \n<\/td>\n<td><p>VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.<\/p>\n<!-- Time to render link large description section of link id 23759: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_VarScan> How to use <\/a>\n<!-- Time to render notes section of link id 23759: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23759: 0.00011682510375977 --> \n<tr><td><a href=\"https:\/\/github.com\/10XGenomics\/vartrix\" id=\"link-24860\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VarTrix<\/a>\n<!-- Time to render name section of link id 24860: 3.0994415283203E-6 --> \n<\/td>\n<td><p>VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.<\/p>\n<!-- Time to render link large description section of link id 24860: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24860: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24860: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/cc2qe\/vawk\" id=\"link-23839\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vawk<\/a>\n<!-- Time to render name section of link id 23839: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An awk-like VCF parser<\/p>\n<!-- Time to render link large description section of link id 23839: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 23839: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23839: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/github.com\/AndersenLab\/VCF-kit\" id=\"link-24755\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">VCF-kit<\/a>\n<!-- Time to render name section of link id 24755: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Assorted utilities for the variant call format.<\/p>\n<!-- Time to render link large description section of link id 24755: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24755: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24755: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/mskcc\/vcf2maf\" id=\"link-24577\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcf2maf<\/a>\n<!-- Time to render name section of link id 24577: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms.<\/p>\n<!-- Time to render link large description section of link id 24577: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcf2maf> How to use <\/a>\n<!-- Time to render notes section of link id 24577: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24577: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/pangenome\/vcfbub\" id=\"link-26100\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcfbub<\/a>\n<!-- Time to render name section of link id 26100: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Popping bubbles in vg deconstruct VCFs.<\/p>\n<!-- Time to render link large description section of link id 26100: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcfbub> How to use <\/a>\n<!-- Time to render notes section of link id 26100: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26100: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/vcflib\/vcflib\" id=\"link-24578\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vcflib<\/a>\n<!-- Time to render name section of link id 24578: 2.1457672119141E-6 --> \n<\/td>\n<td><p>C++ library and cmdline tools for parsing and manipulating VCF files.<\/p>\n<!-- Time to render link large description section of link id 24578: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vcflib> How to use <\/a>\n<!-- Time to render notes section of link id 24578: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24578: 0.0001070499420166 --> \n<tr><td><a href=\"https:\/\/github.com\/biopet\/vcfstats\" id=\"link-26194\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vcfstats<\/a>\n<!-- Time to render name section of link id 26194: 2.1457672119141E-6 --> \n<\/td>\n<td><p>Vcfstats is a tool that can generate metrics from a vcf file.<\/p>\n<!-- Time to render link large description section of link id 26194: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vcfstats> How to use <\/a>\n<!-- Time to render notes section of link id 26194: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 26194: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/vgteam\/vg\" id=\"link-24581\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">vg<\/a>\n<!-- Time to render name section of link id 24581: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.<\/p>\n<!-- Time to render link large description section of link id 24581: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_vg> How to use <\/a>\n<!-- Time to render notes section of link id 24581: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24581: 0.00011014938354492 --> \n<tr><td><a href=\"https:\/\/github.com\/atks\/vt\" id=\"link-25487\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Vt<\/a>\n<!-- Time to render name section of link id 25487: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool set for short variant discovery in genetic sequence data.<\/p>\n<!-- Time to render link large description section of link id 25487: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Vt> How to use <\/a>\n<!-- Time to render notes section of link id 25487: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25487: 0.00011110305786133 --> \n<tr><td><a href=\"https:\/\/github.com\/whatshap\/whatshap\/\" id=\"link-24592\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">WhatsHap<\/a>\n<!-- Time to render name section of link id 24592: 2.1457672119141E-6 --> \n<\/td>\n<td><p>WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.<\/p>\n<!-- Time to render link large description section of link id 24592: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_WhatsHap> How to use <\/a>\n<!-- Time to render notes section of link id 24592: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24592: 0.0001070499420166 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1163\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => publish\n        )\n\n    [orderby] => Array\n        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[query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0015380382537842-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1163 level0\"><!-- Div Category --><div id=\"systems-biology\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Systems biology<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/jotech\/gapseq\" id=\"link-26234\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">gapseq<\/a>\n<!-- Time to render name section of link id 26234: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks.<\/p>\n<!-- Time to render link large description section of link id 26234: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_gapseq> How to use <\/a>\n<!-- Time to render notes section of link id 26234: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 26234: 0.00029802322387695 --> \n<tr><td><a href=\"https:\/\/github.com\/tanghaibao\/goatools\" id=\"link-25258\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">goatools<\/a>\n<!-- Time to render name section of link id 25258: 5.9604644775391E-6 --> \n<\/td>\n<td><p>Python library to handle Gene Ontology (GO) terms.<\/p>\n<!-- Time to render link large description section of link id 25258: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_goatools> How to use <\/a>\n<!-- Time to render notes section of link id 25258: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25258: 0.00028085708618164 --> \n<tr><td><a href=\"https:\/\/github.com\/thh32\/MiMiC2\" id=\"link-26236\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MiMiC2<\/a>\n<!-- Time to render name section of link id 26236: 6.1988830566406E-6 --> \n<\/td>\n<td><p>MiMiC2 is a bioinformatic pipeline for the selection of a few microbial genomes that functionally represent an entire ecosystem, termed a synthetic community (SynCom).<\/p>\n<!-- Time to render link large description section of link id 26236: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MiMiC2> How to use <\/a>\n<!-- Time to render notes section of link id 26236: 2.1457672119141E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26236: 0.00029611587524414 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                    [terms] => 1150\n                    [include_children] => \n                )\n\n        )\n\n    [post_status] => Array\n        (\n            [0] => 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PromoTech\n            [post_excerpt] => \n            [post_status] => publish\n            [comment_status] => closed\n            [ping_status] => closed\n            [post_password] => \n            [post_name] => promotech\n            [to_ping] => \n            [pinged] => \n            [post_modified] => 2024-11-20 13:05:07\n            [post_modified_gmt] => 2024-11-20 12:05:07\n            [post_content_filtered] => \n            [post_parent] => 0\n            [guid] => https:\/\/bioinfo.genotoul.fr\/?post_type=link_library_links&#038;p=25544\n            [menu_order] => 0\n            [post_type] => link_library_links\n            [post_mime_type] => \n            [comment_count] => 0\n            [filter] => raw\n        )\n\n    [comment_count] => 0\n    [current_comment] => -1\n    [found_posts] => 1\n    [max_num_pages] => 0\n    [max_num_comment_pages] => 0\n    [is_single] => \n    [is_preview] => \n    [is_page] => \n    [is_archive] => 1\n    [is_date] => \n    [is_year] => \n    [is_month] => \n    [is_day] => \n    [is_time] => \n    [is_author] => \n    [is_category] => \n    [is_tag] => \n    [is_tax] => 1\n    [is_search] => \n    [is_feed] => \n    [is_comment_feed] => \n    [is_trackback] => \n    [is_home] => \n    [is_privacy_policy] => \n    [is_404] => \n    [is_embed] => \n    [is_paged] => \n    [is_admin] => \n    [is_attachment] => \n    [is_singular] => \n    [is_robots] => \n    [is_favicon] => \n    [is_posts_page] => \n    [is_post_type_archive] => \n    [query_vars_hash:WP_Query:private] => 1d8f423d64d8a5ef5182b3f1995954c7\n    [query_vars_changed:WP_Query:private] => \n    [thumbnails_cached] => \n    [allow_query_attachment_by_filename:protected] => \n    [stopwords:WP_Query:private] => \n    [compat_fields:WP_Query:private] => Array\n        (\n            [0] => query_vars_hash\n            [1] => query_vars_changed\n        )\n\n    [compat_methods:WP_Query:private] => Array\n        (\n            [0] => init_query_flags\n            [1] => parse_tax_query\n        )\n\n)\n-->\n\n\n<!-- Link Query Execution Time: 0.0014660358428955-->\n\n<!-- showonecatmode: , AJAXnocatset: , nocatonstartup: --><div class=\"LinkLibraryCat LinkLibraryCat1150 level0\"><!-- Div Category --><div id=\"transcription-factors\"><!-- Div Category Name --><div class=\"linklistcatname\"><!-- Div Cat Name --><span class=\"linklistcatclass\">Transcription factors<\/span><span class=\"linklistcatnamedesc\"><\/span><\/div><!-- DivOrHeader --><\/div><!-- Div Category Name -->\n\t<table class='linklisttable'>\n<div class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/BioinformaticsLabAtMUN\/PromoTech\" id=\"link-25544\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PromoTech<\/a>\n<!-- Time to render name section of link id 25544: 6.1988830566406E-6 --> \n<\/td>\n<td>Promotech is a machine-learning-based classifier trained to generate a model that generalizes and detects promoters in a wide range of bacterial species.\n<!-- Time to render link large description section of link id 25544: 1.9073486328125E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Promotech> How to use <\/a>\n<!-- Time to render notes section of link id 25544: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 25544: 0.00031113624572754 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => link_library_category\n                    [field] => term_id\n                 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class=\"linklisttableheaders\"><tr><th><div class=\"linklistcolumnheader\">Application<\/div><\/th><th><div class=\"linklistcolumnheader\">Description<\/div><\/th><th><div class=\"linklistcolumnheader\">Availability\/Use<\/div><\/th><\/tr><\/div>\n<tr><td><a href=\"https:\/\/github.com\/willros\/bam2plot\" id=\"link-25605\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">bam2plot<\/a>\n<!-- Time to render name section of link id 25605: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Make coverage plots from bam files.<\/p>\n<!-- Time to render link large description section of link id 25605: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_bam2plot> How to use <\/a>\n<!-- Time to render notes section of link id 25605: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25605: 0.0001990795135498 --> \n<tr><td><a href=\"https:\/\/sourceforge.net\/projects\/cvit\/\" id=\"link-24190\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CVIT<\/a>\n<!-- Time to render name section of link id 24190: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps.<\/p>\n<!-- Time to render link large description section of link id 24190: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_CVIT> How to use <\/a>\n<!-- Time to render notes section of link id 24190: 1.1920928955078E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24190: 0.00028705596923828 --> \n<tr><td><a href=\"https:\/\/github.com\/lidaof\/g3d\" id=\"link-25033\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">g3d<\/a>\n<!-- Time to render name section of link id 25033: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Genomics 3D visualizer tool sets.<\/p>\r\n<p><code class=\"docutils literal notranslate\"><span class=\"pre\">g3d<\/span><\/code>\u00a0is a binary file format for storing genomic 3D structure data,\u00a0<code class=\"docutils literal notranslate\"><span class=\"pre\">g3d<\/span><\/code>\u00a0is short for genomic 3D format.<\/p>\n<!-- Time to render link large description section of link id 25033: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_g3d> How to use <\/a>\n<!-- Time to render notes section of link id 25033: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25033: 0.00020384788513184 --> \n<tr><td><a href=\"https:\/\/github.com\/yeeus\/GCI.git\" id=\"link-25561\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GCI<\/a>\n<!-- Time to render name section of link id 25561: 3.0994415283203E-6 --> \n<\/td>\n<td>Genome Continuity Inspector (GCI) is an assembly assessment tool for high-quality genomes (e.g. T2T genomes), in base resolution.\n<!-- Time to render link large description section of link id 25561: 0 --> \n<\/td>\n<td><br><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GCI> How to use <\/a>\n<!-- Time to render notes section of link id 25561: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25561: 0.00019717216491699 --> \n<tr><td><a href=\"https:\/\/github.com\/ggonnella\/gfaviz\" id=\"link-25600\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">GfaViz<\/a>\n<!-- Time to render name section of link id 25600: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Graphical interactive tool for the visualization of sequence graphs in GFA format.<\/p>\n<!-- Time to render link large description section of link id 25600: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GfaViz> How to use <\/a>\n<!-- Time to render notes section of link id 25600: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25600: 0.0001990795135498 --> \n<tr><td><a href=\"https:\/\/github.com\/achtman-lab\/GrapeTree\" id=\"link-24260\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">GrapeTree<\/a>\n<!-- Time to render name section of link id 24260: 4.0531158447266E-6 --> \n<\/td>\n<td><p>GrapeTree is a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.<\/p>\n<!-- Time to render link large description section of link id 24260: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_GrapeTree> How to use <\/a>\n<!-- Time to render notes section of link id 24260: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24260: 0.00018191337585449 --> \n<tr><td><a href=\"https:\/\/bitbucket.org\/dmarnetto\/haplostrips\/src\/master\/\" id=\"link-25020\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Haplostrips<\/a>\n<!-- Time to render name section of link id 25020: 3.0994415283203E-6 --> \n<\/td>\n<td><p>Haplostrips produce plots that depict variants in a genomic window among different samples. Visualize similarities between haplotypes with respect to a reference haplotype through haplotype clustering and sorting, useful for revealing hidden population structure.<\/p>\n<!-- Time to render link large description section of link id 25020: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Haplostrips> How to use <\/a>\n<!-- Time to render notes section of link id 25020: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25020: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/marbl\/harvest-tools\" id=\"link-25350\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">HarvestTools<\/a>\n<!-- Time to render name section of link id 25350: 4.0531158447266E-6 --> \n<\/td>\n<td><p>HarvestTools is a utility for creating and interfacing with Gingr files, which are efficient archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.<\/p>\n<!-- Time to render link large description section of link id 25350: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HarvestTools> How to use <\/a>\n<!-- Time to render notes section of link id 25350: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25350: 0.00018095970153809 --> \n<tr><td><a href=\"https:\/\/hyphy.org\/\" id=\"link-23645\" class=\"track_this_link  featured\" rel=\"noopener noreferrer\" target=\"_blank\">HyPhy<\/a>\n<!-- Time to render name section of link id 23645: 3.0994415283203E-6 --> \n<\/td>\n<td><p>HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses.<\/p>\n<!-- Time to render link large description section of link id 23645: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_HyPhy> How to use <\/a>\n<!-- Time to render notes section of link id 23645: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 23645: 0.00018501281738281 --> \n<tr><td><a href=\"https:\/\/github.com\/Superzchen\/iFeature\" id=\"link-26174\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">iFeature<\/a>\n<!-- Time to render name section of link id 26174: 3.0994415283203E-6 --> \n<\/td>\n<td><p>iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. Install with Spann model: https:\/\/github.com\/nicolagulmini\/spaan<\/p>\n<!-- Time to render link large description section of link id 26174: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_iFeature> How to use <\/a>\n<!-- Time to render notes section of link id 26174: 1.9073486328125E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 26174: 0.00018405914306641 --> \n<tr><td><a href=\"https:\/\/github.com\/mapequation\/infomap\" id=\"link-24833\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Infomap<\/a>\n<!-- Time to render name section of link id 24833: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Multi-level network clustering based on the Map Equation.<\/p>\n<!-- Time to render link large description section of link id 24833: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24833: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24833: 0.00018310546875 --> \n<tr><td><a href=\"https:\/\/github.com\/mkirsche\/Jasmine\" id=\"link-25042\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Jasmine<\/a>\n<!-- Time to render name section of link id 25042: 3.0994415283203E-6 --> \n<\/td>\n<td><p dir=\"auto\">JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges. This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.<\/p>\r\n<p dir=\"auto\">Manual : <a href=\"https:\/\/github.com\/mkirsche\/Jasmine\/wiki\/Jasmine-User-Manual\">Jasmine User Manual \u00b7 mkirsche\/Jasmine Wiki \u00b7 GitHub<\/a><\/p>\r\n<p dir=\"auto\">Jasmine also includes a module for automating the creation of\u00a0<a href=\"http:\/\/software.broadinstitute.org\/software\/igv\/\" rel=\"nofollow\">IGV<\/a>\u00a0screenshots of variants of interest.<\/p>\n<!-- Time to render link large description section of link id 25042: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_Jasmine> How to use <\/a>\n<!-- Time to render notes section of link id 25042: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25042: 0.00019502639770508 --> \n<tr><td><a href=\"https:\/\/github.com\/liulab-dfci\/MAGeCK\" id=\"link-25102\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">MAGeCK<\/a>\n<!-- Time to render name section of link id 25102: 3.814697265625E-6 --> \n<\/td>\n<td><p>Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.<br \/>\r\nMAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR\/Cas9 screens.<br \/>\r\nMAGeCKFlute (R package):Integrative analysis pipeline for pooled CRISPR functional genetic screens<\/p>\r\n<p>Manual and video tutorials : <a href=\"https:\/\/bitbucket.org\/liulab\/mageck-vispr\/src\/master\/\">liulab \/ mageck-vispr \u2014 Bitbucket<\/a><\/p>\n<!-- Time to render link large description section of link id 25102: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_MAGeCK> How to use <\/a>\n<!-- Time to render notes section of link id 25102: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25102: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/forgemia.inra.fr\/metexplore\/met4j\" id=\"link-24713\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">Met4j<\/a>\n<!-- Time to render name section of link id 24713: 2.8610229492188E-6 --> \n<\/td>\n<td><p>Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.<\/p>\n<!-- Time to render link large description section of link id 24713: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24713: 1.9073486328125E-6 --> \n<\/td><\/tr>\n<!-- Time to render link id 24713: 0.0002131462097168 --> \n<tr><td><a href=\"https:\/\/github.com\/schneebergerlab\/plotsr\" id=\"link-24456\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">plotsr<\/a>\n<!-- Time to render name section of link id 24456: 4.0531158447266E-6 --> \n<\/td>\n<td><p>Tool to plot synteny and structural rearrangements between genomes.<\/p>\n<!-- Time to render link large description section of link id 24456: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_plotsr> How to use <\/a>\n<!-- Time to render notes section of link id 24456: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 24456: 0.0001828670501709 --> \n<tr><td><a href=\"https:\/\/github.com\/sanger-tol\/PretextView\" id=\"link-25527\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">PretextView<\/a>\n<!-- Time to render name section of link id 25527: 2.1457672119141E-6 --> \n<\/td>\n<td><p>OpenGL Powered Pretext Contact Map Viewer.<\/p>\n<!-- Time to render link large description section of link id 25527: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_PretextView> How to use <\/a>\n<!-- Time to render notes section of link id 25527: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25527: 0.00010013580322266 --> \n<tr><td><a href=\"https:\/\/github.com\/isabelschober\/proteinortho_curves\" id=\"link-25230\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">proteinortho_curves<\/a>\n<!-- Time to render name section of link id 25230: 1.9073486328125E-6 --> \n<\/td>\n<td><p>Draw pan- and core-genome curves from proteinortho output<\/p>\n<!-- Time to render link large description section of link id 25230: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_proteinortho_curves> How to use <\/a>\n<!-- Time to render notes section of link id 25230: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25230: 9.7990036010742E-5 --> \n<tr><td><a href=\"https:\/\/github.com\/Illumina\/REViewer\" id=\"link-25729\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">REViewer<\/a>\n<!-- Time to render name section of link id 25729: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A tool for visualizing alignments of reads in regions containing tandem repeats<\/p>\n<!-- Time to render link large description section of link id 25729: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_REViewer> How to use <\/a>\n<!-- Time to render notes section of link id 25729: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25729: 0.00010800361633301 --> \n<tr><td><a href=\"https:\/\/github.com\/CJ-Chen\/TBtools-II\" id=\"link-25247\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">TBtools-II<\/a>\n<!-- Time to render name section of link id 25247: 1.9073486328125E-6 --> \n<\/td>\n<td><p>GUI\/CommandLine Tool Box for biologistists to utilize NGS data.<\/p>\n<!-- Time to render link large description section of link id 25247: 9.5367431640625E-7 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_TBtools-II> How to use <\/a>\n<!-- Time to render notes section of link id 25247: 0 --> \n<\/td><\/tr>\n<!-- Time to render link id 25247: 0.00010895729064941 --> \n<tr><td><a href=\"https:\/\/github.com\/atanunq\/viu\" id=\"link-25337\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">viu<\/a>\n<!-- Time to render name section of link id 25337: 1.9073486328125E-6 --> \n<\/td>\n<td><p>A small command-line application to view images from the terminal written in Rust.<\/p>\n<!-- Time to render link large description section of link id 25337: 1.1920928955078E-6 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=index.php\/how-to-use-3?software=How_to_use_SLURM_viu> How to use <\/a>\n<!-- Time to render notes section of link id 25337: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 25337: 0.00010895729064941 --> \n\t<\/table>\n<\/div><!-- Div End Category -->\n\n<!-- Link Query: Array\n(\n    [post_type] => link_library_links\n    [posts_per_page] => -1\n    [tax_query] => Array\n        (\n            [0] => Array\n                (\n                    [taxonomy] => 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link id 24176: 2.1457672119141E-6 --> \n<\/td>\n<td><p>chimerascan is a software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.<\/p>\n<!-- Time to render link large description section of link id 24176: 0 --> \n<\/td>\n<td><strong>Genobioinfo Cluster: <\/strong> <a href=https:\/\/bioinfo.genotoul.fr\/index.php\/ask-for\/install-soft\/> Ask for Install<\/a>\n<!-- Time to render notes section of link id 24176: 9.5367431640625E-7 --> \n<\/td><\/tr>\n<!-- Time to render link id 24176: 0.00010919570922852 --> \n<tr><td><a href=\"https:\/\/culebront-pipeline.readthedocs.io\/en\/latest\/\" id=\"link-24189\" class=\"track_this_link \" rel=\"noopener noreferrer\" target=\"_blank\">CulebrONT<\/a>\n<!-- Time to render name section of link id 24189: 1.9073486328125E-6 --> \n<\/td>\n<td><p>An open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple assembly tools in parallel, giving you the possibility of circularise, polish, and 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If you need&#46;&#46;&#46;<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":2208,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"page-templates\/child-menu.php","meta":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v20.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Software - genotoul-bioinfo<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bioinfo.genotoul.fr\/index.php\/resources-2\/softwares\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Software - genotoul-bioinfo\" \/>\n<meta property=\"og:description\" content=\"The GenoToul bioinformatics platform provides access to high-performance computing resources with softwares already installed to ease its usage. An exhaustive list is provided hereunder. Software are updated only upon user request. 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