Software

3D de novo assembly (3D-DNA) pipeline.

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads.

Allele CAlling proCedure for Illumina Amplicon sequencing data: This workflow aims at extracting allele information out of paired-end Illumina FASTQC files.

This program was developed to remove residual adapter sequences from next generation sequencing reads. The program handles both single end and paired end data.

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.

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).

The ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture

Phasing and scaffolding polyploid genomes based on Hi-C data

AmpliSAT (Amplicon Sequencing Analysis Tools) are a set of online tools that make easy the analysis of Amplicon Sequencing experiments.

Identify IBD segments between pairs of individuals in ancient human DNA data.

The software package ancIBD detects Identity-by-Descent (IBD) segments in typical human aDNA data, implementing an algorithm described in this preprint. The input data are imputed and phased genotype data. The default parameters of ancIBD are optimized for imputed data using the software GLIMPSE using the 1000 Genome haplotype reference panel.

Software documentation here.

An integrated tool for Structural Variations annotation and ranking.

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.

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

The distribution is a parallel wrapper around the Arrow consensus framework within the SMRT Analysis Software

Ascertained Sequentially Markovian Coalescent (contains ASMC and an extension, FastSMC, together with python bindings for both)

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).

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.

Augustus is a program that predicts genes in eukaryotic genomic sequences

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.

AvP performs automatic detection of HGT candidates within a phylogenetic framework.

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.

BAMscorer can be used to conduct genomic assignment tests from BAM files. Assignments can be done on genomic regions, inversions, and whole-genome datasets.

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

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.

a short read aligner, as well as various other bioinformatic tools.

utilities for variant calling and manipulating VCFs and BCFs.

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

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.

Simple utility programs for manipulating text files, especially VCF files.

BEAGLE-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages

BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.

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.

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.

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.

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.

Highly parallel construction and indexing of colored and compacted de Bruijn graphs.

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.

BiSCoT is a tool that aims to improve the contiguity of scaffolds and contigs generated after a Bionano scaffolding.

BISulfite-seq CUI Toolkit (BISCUIT) is a utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data.

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Python program to query .fasta files against the different databases of www.boldsystems.org

An even better Python program to query .fasta files against the COI database of www.boldsystems.org

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).

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.

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.

BRAKER(1,2,3) is a tool for fully automated genome annotation with GeneMark-ET and AUGUSTUS

Bridger is an efficient de novo trascriptome assembler for RNA-Seq data.

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.

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.

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.

A script to turn a set of BUSCO results into a directory of multisequence FASTA files.

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.

Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster.

Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit.

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).

AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets.

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.

Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Cell Ranger ARC's pipelines analyze sequencing data produced from Chromium Single Cell Multiome ATAC + Gene Expression.

CENSOR compares and masks protein or nucleotide sequences.

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.

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

CHEUI (Methylation (CH₃) 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).

This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.

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.

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset

A tool to detect and quantify full-length circRNA isoforms from circFL-seq.

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.

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.

A software package that performs efficient inference of recombination in bacterial genomes.

cnD is a program to detect copy number variants from short-read sequence data.

A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.

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.

Read the full documentation at: http://cnvkit.readthedocs.io

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.

Conterminator is an efficient method for detecting incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison.

ContScout is a pipeline developed for the identification and removal of contaminating sequences in draft genomes.

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.

CRABS (Creating Reference databases for Amplicon-Based Sequencing) is a versatile software program that generates curated reference databases for metagenomic analysis.

CRISPOR predicts off-targets in the genome, ranks guides, highlights problematic guides, designs primers and helps with cloning.

A cross-platform, efficient and practical CSV/TSV toolkit in Golang.

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.

Estimation of current effective population using artificial neural networks.

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.

Long read based human genomic structural variation detection with cuteSV.

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage.

DamageProfiler calculates damage profiles of mapped reads and provides a graphical as well as text based representation.

It creates

• damage plots
• fragment length distribution
• read identity distribution
• base frequency table of reference
• table of different base misincorporations and their occurrences

A complete framework for identifying quantitatively differential compartments from Hi-C and Micro-C data.

DARIC, 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 BMC Genomics.

Dasel (short for data-selector) allows you to query and modify data structures using selector strings.

GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.

An integrated tool for rapid prophage detection and annotation.

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.

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.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Genetic multiplexing of barcoded single cell RNA-seq

devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing (scRNA-seq).

DFE-alpha was initially written to estimate the distribution of fitness effects (DFE) of new deleterious mutations using within-species nucleotide polymorphism data.

Accelerated BLAST compatible local sequence aligner.

Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressor.

De novo RNA-seq Assembly Pipeline

Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

Ensemble Enzyme Prediction Pipeline.

A fully automated TE curation and annotation pipeline.

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

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.

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.

The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).

EvaLuation of Error Correction Tools for lOng Reads.

elPrep is a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.

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.

EMMAX is 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.

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.

EPIK is a program for rapid alignment-free phylogenetic placement.

ERPIN (Easy RNA Profile IdentificatioN) is an RNA motif search program developped by Daniel Gautheret and André Lambert.

est-sfs implements a maximum likelihood method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities for DNA sequence data.

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets.

evalAdmix allows to evaluate the results of an admixture analysis (i.e. the result of applying ADMIXTURE, STRUCTURE, NGSadmix and similar).

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.

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.

A generic tool for sequence alignment.

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

Falcon: a set of tools for fast aligning long reads for consensus and assembly

FASTA is a sequence similarity search tool which uses heuristics for fast local alignment searching.

finds the overall composition of sequences in a FASTA file

FASTA Length finds the lengths of sequences in a FASTA file.

C code to validate a fasta file.

A simple command line tool to add prefixes to FASTA headers.

A set of utilities to calculate the median number of times the k-mers in a sequence of interest occur across the whole set.

A tool designed to provide fast all-in-one preprocessing for FastQ files.

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.

This program can filter FASTQ files produced by CASAVA 1.8, and keep/discard reads based on this filter flag.

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.

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

FCS-GX detects contamination from foreign organisms in genome sequences. This tool is one module within the NCBI Foreign Contamination Screening (FCS) program suite.

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.

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.

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.

FMLRC2 performs error correction/polishing of long erroneous sequences with accurate short reads. As such, it can be used as both an error-correction tool <1> for raw long reads (ex. Oxford Nanopore) and a polishing tool <2> for de novo assemblies.

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.

It is a re-implementation of FragGeneScan in Rust.

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.

Genomics 3D visualizer tool sets.

g3d is a binary file format for storing genomic 3D structure data, g3d is short for genomic 3D format.

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.

This is an alternative and an upgrade of the widely used PSMC method, which infers population size trajectories from VCF files.

The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo, using the abundant pair relationships of short reads.

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.

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.

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.

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.

A set of very optimized tools for indexing/querying huge genomes/files.

GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.

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.

a semi-supervised version of GeneMark-ES, called GeneMark-ET that uses RNA-Seq reads to improve training.

Fast genome analysis from unassembled short reads

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.

Collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named "gt".

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.

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.

gget enables efficient querying of genomic reference databases.

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).

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST SequencesGSNAP: Genomic Short-read Nucleotide Alignment Program

Python library to handle Gene Ontology (GO) terms.

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.

Gotree is a set of command line tools and an API to manipulate phylogenetic trees.

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.

Seed-and-extend program for aligning long error-prone reads to genome graphs.

Unzip assembly graphs with Hi-C data and/or long reads.

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.

Convert HAL to vg-compatible sequence graph.

Efficient High-throughput ANNOtation of protein coding genes in eukaryote genomes.

The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.

NGS viral assembly and population genetics.

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.

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.

Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.

Find likely coding segments in DNA using composition-normalised hexamer tables.

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

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.

A fast and efficient tool for converting chromatin interaction data between genome assemblies.

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome.

De novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.

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).

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).

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.  It is a collection of command line programs for unix-style operating systems written in Perl and C++.

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

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 (Krueger, 2015), and assembled using the iterative baited assembly (IBA) Python script which employs USEARCH v. 7.0 (Edgar, 2010) and Bridger v. 2014-12-01 (Chang et al., 2015) to assemble loci for each taxon. MAFFT v. 7.245 (Katoh and Standley, 2013) was used to align assembled sequences, and the probe and flanking regions were separated with the Python script Extract_probe_region.py (Breinholt et al., 2018).

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.

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.

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.

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).

Multi-level network clustering based on the Map Equation.

A tool for evaluate long-read de novo assembly results.

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.

IPK is a tool for computing phylo-k-mers for a fixed phylogeny.

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.

Efficient phylogenomic software by maximum likelihood

Detecting intron retention from RNA-Seq experiments

A module which corrects the sequences of structural variant calls (currently only insertions).

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.

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.

Manual : Jasmine User Manual · mkirsche/Jasmine Wiki · GitHub

Jasmine also includes a module for automating the creation of IGV screenshots of variants of interest.

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.

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.

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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.

A Fast, Accurate, and User-Friendly Ortholog-Finding Algorithm

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

A fast and space-saving multi-threaded k-mer frequency statistics algorithm

UCSC command line bioinformatic utilities

KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.

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.

A fast k-mer counter written in Rust.

KmerGenie estimates the best k-mer length for genome de novo assembly.

A library for running k-mers based GWAS.

KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

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.

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.

kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.

LAST finds similar regions between sequences.

A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically.

LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.

LDhelmet performs statistical inference for fine-scale variable recombination rate estimation.

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.

Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.

La Jolla Assembler (LJA) is a tool for genome assembly from HiFI reads based on de Bruijn graphs.

LOCALIZER is a machine learning method for predicting the subcellular localization of both plant proteins and pathogen effectors in the plant cell.

Protein Subcelullar Localization Sequenced-Based Predictor

A sequence-quality aware, ultra-sensitive variant caller for NGS data.

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.

A de-novo tool for detecting simple tandem repeats using self-supervised hidden Markov models.

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.

 LR_Gapcloser is a gap closing tool using uncorrected or corrected long reads generated from Pacbio platform or Nanopore platform. 

TGS scaffolding . Improving draft genomes using long noisy reads.

LS^X is a script in R that runs the LS³ and LS⁴ 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 here or in the papers), 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 “flagged” (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.

MACH is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Model-based Analysis of ChIP-Seq

A Multi AgEnt STability pRedictiOn tool for changes in unfolding free energy upon point mutation.

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 ΔΔG 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.

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.
MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
MAGeCKFlute (R package):Integrative analysis pipeline for pooled CRISPR functional genetic screens

Manual and video tutorials : liulab / mageck-vispr — Bitbucket

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.

This is a version of ALDER (http://groups.csail.mit.edu/cb/alder/) that has been modified to allow multiple admixture events.

MALT (MEGAN alignment tool) is an extension of MEGAN (metagenome analyzer).
MALT 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.

tracking and quantifying damage patterns in ancient DNA sequences.

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.

Fast genome and metagenome distance estimation using MinHash.

documentation : Publications — Mash 2.0 documentation

Create a tree using Mash distances.

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn 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)

MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

This program is designed to call m6A from nanopore data using the differences between measured and expected currents.

MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads.

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.

A tool to merge assembled contigs, long reads from metagenomic sequencing runs

MEtaGenome ANalyzer : Metagenomic data analysis : taxonomic and functionnal (SEED and KEGG classification) analysis. 

Evaluate genome assemblies with k-mers and more

A genomic k-mer counter (and sequence utility) with nice features.

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.

A fast and accurate ancient DNA damage toolkit for metagenomic data.

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.

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.

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.

A lightweight assembler for long and accurate metagenomics reads.

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

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.

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.

A segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole-genome datasets.

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.

Identification of differentially methylated regions between multiple epigenomes from BS-treated read mappings via methylated region calling.

A mitochondrial genome analysis toolkit.

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

Ultrafast de novo assembly for long noisy reads (though having no consensus step).

Experimental tool to find approximate mapping positions between long sequences

Aligning proteins to genomes with splicing and frameshift.

Use MIPgen to design custom mip panels for target enrichment of moderate to high complexity DNA targets ranging from 120 to 250bp in size.

Whole genome shotgun and EST sequence assembler for Sanger, 454, and Solexa / Illumina.

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.

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.

MitoHPC : Mitochondrial High Performance Caller. For Calling Mitochondrial Homoplasmies and Heteroplasmies.

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.

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge proteins/nucleotide sequence sets.

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.

A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.

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.

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.

MOSAIK is a reference-guided assembler comprising of two main modular programs

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.

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.

A tool for single-locus species delimitation.

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.

A program for generating samples under neutral models.

MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data.

This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data

msprime is a population genetics simulator based on tskit. 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 tskit) under a variety of genome sequence evolution models.

Please see the documentation for more details

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.

Aggregate results from bioinformatics analyses across many samples into a single report.

MUMmer is a package for rapidly aligning entire genomes, whether in complete or draft form.

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).

MZmine is an open-source software for mass-spectrometry data processing.

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.

Compare multiple runs of long read sequencing data and alignments.

Filtering and trimming of Oxford Nanopore sequencing data

Plotting tool for Oxford Nanopore sequencing data and alignments.

A nanopore consensus algorithm using a signal-level hidden Markov model. Signal-level algorithms for MinION data.

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.

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

Similarity search against databanks.

Similarity search against databanks.

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 NCBI Datasets web interface.

NCBI portable software toolkit

NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.

NetLogo is a multi-agent programmable modeling environment.

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.

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.

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).

Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

This module provide access to workflows nf-core, there are automatically downloaded into your home.

More info at nf-core/config page.

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

ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account.

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.

Tools for next-generation sequencing analysis.

NLRtracker extracts and functionally annotates NLRs from protein or transcript files based on the core features found in the RefPlantNLR dataset.

NOVOPlasty is a de novo assembler and variance caller for short circular genomes.

NSEG is used to mask nucleic acid sequences, needed by RepeatScout.

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).

Oases 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.

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.

The OMA (Orthologous MAtrix) database is a well-established resource for identifying orthologs among publicly available complete genomes.

An alignment tool for optical mapping data.

ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore fast5 file format.

The ORGanelle ASseMbler aims to target the assembling of small sequences over-represented in a whole genome shotgun sequence dataset.

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.

Standalone pipeline for delineation of orthologs.

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification.

pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment.

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.

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.

A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph.

PanTools is a toolkit for comparative analysis of large number of genomes.

GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

PartitionFinder is free open source software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.

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.

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.

A workflow for integrating ancient lineages into present-day phylogenies.

Tools for inferring and interpreting phylogenetic trees

Parallelized blat with multi-threads support.

PacBio BAM toolkit

PCAdmix is a method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes.  The method considers data chromosome by chromosome.

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.

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.

Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuraccy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus.

Pangenome graph builder.

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.

Small utility scripts to query the PHASTER API endpoint, to identify and annotate prophage sequences within bacterial genomes and plasmids.

The Phi Test is a simple, rapid, and statistically efficient test for recombination.

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction and molecular dating using protein and nucleic acid alignments.

PhyloBayes (Lartillot et al, 2009) is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. With MPI.

phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

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.

phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.

PhyML is a phylogeny software based on the maximum-likelihood principle.

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.

Genomic repeat analysis software.

Pilon is an automated genome assembly improvement and variant detection tool.

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.

Software for prediction of plasmid sequences in metagenomic assemblies.

An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.

plassembler is a program that is designed for automated & fast assembly of plasmids in bacterial genomes that have been hybrid sequenced with long read & paired-end short read sequencing.

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.

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.

A model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data.

Polypolish is a tool for polishing genome assemblies with short reads.

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.

Population-scale detection of novel-sequence insertions.

Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs.

PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D with a sliding window approach for chromosomes or for set of genes.

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.

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).

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.

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.

Prediction of glycosylphosphatidylinositol-anchors in proteins based on HMMs and SVMs.

Software for predicting library complexity and genome coverage in high-throughput sequencing.

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps. Full suite of Pretext tools.

OpenGL Powered Pretext Contact Map Viewer.

Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction").

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.

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.

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.

Prost! (PRocessing Of Short Transcripts) can analyze smallRNA sequencing data generated on any sequencing platform. Prost! does 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 Prost! run, allowing an accurate analysis of an entire dataset. After grouping the processed reads by genomic location, Prost! then annotates them using a user-defined annotation database (public or personal annotation database).

Proteinortho is a tool to detect orthologous genes within different species.

Draw pan- and core-genome curves from proteinortho output

PSAURON is a machine learning model for rapid assessment of protein coding gene annotation.

Detection of pseudogene candidates in bacterial and archaeal genomes.

This software package infers population size history from a diploid sequence
using the Pairwise Sequentially Markovian Coalescent (PSMC) model.

purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.