Here is the list of available command line software.
Categories
All
Expression analysis
- Librairies and other tools
- SNP and structural variations
- Repeats
- Proteins
- Phylogeny / Metagenomic
- Sequences cleaning
- Pattern
- Genetic map
- Assembly
- ncRNA
- Annotation
- Sequences alignment
- Genomic association studies
- Mathematic
- Population genetics
- ChIP-Seq analysis
- RAD-Seq analysis
Nucleic acid folding
13.09.2012
miRDeep-P,miRDP for short, is a computational tool for analyzing the microRNA (miRNA) transcriptome in plants.
http://sourceforge.net/projects/mirdp/
mirDeep-P
miRDeep-P,miRDP for short, is a computational tool for analyzing the microRNA (miRNA) transcriptome in plants.
http://sourceforge.net/projects/mirdp/
Category: ncRNA
20.02.2012
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.
http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/
mirDeep2
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.
http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/
Category: ncRNA
31.07.2012
miRPara is a SVM-based miRNA prediction tool.
http://159.226.126.177/mirpara/download.htm
miRPara
miRPara is a SVM-based miRNA prediction tool.
http://159.226.126.177/mirpara/download.htm
Category: ncRNA
02.09.2010
Rnammer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project.
http://www.cbs.dtu.dk/services/RNAmmer/
rnammer
Rnammer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project.
http://www.cbs.dtu.dk/services/RNAmmer/
Category: ncRNA
02.09.2010
Search for tRNA genes in genomic sequence.
http://lowelab.ucsc.edu/tRNAscan-SE/
tRNAscan-SE
Search for tRNA genes in genomic sequence.
http://lowelab.ucsc.edu/tRNAscan-SE/
Category: ncRNA
02.09.2010
Vienna RNA package allows RNA Secondary Structure Prediction and Comparison.
http://www.tbi.univie.ac.at/RNA/
viennaRNA
Vienna RNA package allows RNA Secondary Structure Prediction and Comparison.
http://www.tbi.univie.ac.at/RNA/
Category: ncRNA