aaindex

Amino acid indices and similarity matrices

abyss

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

allpaths

De novo assembly of whole-genome shotgun microreads

allpathslg

De novo assembly of whole-genome shotgun microreads

amap

Protein multiple-alignment-based sequence annealing

amos

A Modular, Open-Source whole genome assembler

ApE

ApE - A Plasmid Editor

arb

Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis

ariadne

Protein sequences and profiles comparison

augustus

Eukaryotic gene predictor

bamtools

A programmer's API and an end-user's toolkit for handling BAM files

beast-mcmc

Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences

bedtools

Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats

bfast

Blat-like Fast Accurate Search Tool

biogrep

Multithreading application for matching large sets of patterns against biosequence dbs.

bioperl

Perl tools for bioinformatics - Core modules

bioperl-db

Perl tools for bioinformatics - Perl API that accesses the BioSQL schema

bioperl-network

Perl tools for bioinformatics - Analysis of protein-protein interaction networks

bioperl-run

Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications

biopython

Python modules for computational molecular biology

bioruby

An integrated environment for bioinformatics using the Ruby language

biosql

A generic bioinformatics relational database model

blat

The BLAST-Like Alignment Tool, a fast genomic sequence aligner

blossoc

A linkage disequilibrium association mapping tool

bowtie

An ultrafast memory-efficient short read aligner

bwa

Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner

cd-hit

Clustering Database at High Identity with Tolerance

clustal-omega

Scalable multiple alignment of protein sequences

clustalw

General purpose multiple alignment program for DNA and proteins

clustalw-mpi

A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm

clustalx

Graphical interface for the ClustalW multiple alignment program

consed

Consed: a genome sequence finishing program

cufflinks

Transcript assembly, differential expression, and differential regulation for RNA-Seq

cutg

Codon usage tables calculated from GenBank

dialign-tx

Greedy and progressive approaches for segment-based multiple sequence alignment

diya

Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotation

elph

Estimated Locations of Pattern Hits - Motif finder program

embassy

A meta-package for installing all EMBASSY packages (EMBOSS add-ons)

embassy-cbstools

EMBOSS wrappers for applications from the CBS group

embassy-domainatrix

Protein domain analysis add-on package for EMBOSS

embassy-domalign

Protein domain alignment add-on package for EMBOSS

embassy-domsearch

Protein domain search add-on package for EMBOSS

embassy-emnu

EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications

embassy-esim4

EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA

embassy-hmmer

EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs

embassy-iprscan

InterProScan motif detection add-on package for EMBOSS

embassy-memenew

EMBOSS wrappers for MEME - Multiple Em for Motif Elicitation

embassy-mira

Fragment assembly add-on package for EMBOSS

embassy-mse

EMBOSS integrated version of MSE - Multiple Sequence Screen Editor

embassy-phylipnew

EMBOSS integrated version of PHYLIP - The Phylogeny Inference Package

embassy-signature

Protein signature add-on package for EMBOSS

embassy-structure

Protein structure add-on package for EMBOSS

embassy-topo

EMBOSS integrated version of TOPO - Transmembrane protein display

embassy-vienna

EMBOSS integrated version of the Vienna RNA package - RNA folding

emboss

The European Molecular Biology Open Software Suite - A sequence analysis package

eugene

Eukaryotic gene predictor

exonerate

Generic tool for pairwise sequence comparison

express

Streaming RNA-Seq Analysis

fasta

FASTA is a DNA and Protein sequence alignment software package

fasttree

Fast inference of approximately-maximum-likelihood phylogenetic trees

finchtv

Graphical viewer for chromatogram files

foldingathome

Folding@Home is a distributed computing project for protein folding.

gatk

The Genome Analysis Toolkit

GBrowse

Generic Model Organism Database Project - The Generic Genome Browser

gibbs

Identify motifs, conserved regions, in DNA or protein sequences

glimmer

An HMM-based microbial gene finding system from TIGR

glimmerhmm

An eukaryotic gene finding system from TIGR

gmap

A Genomic Mapping and Alignment Program for mRNA and EST Sequences

goby

A DNA sequencing data management framework

goby-cpp

A DNA sequencing data management framework - C/C++ API

hmmer

Sequence analysis using profile hidden Markov models

iedera

A subset seed design tool for DNA sequence alignment

infernal

Inference of RNA alignments

iqpnni

Important Quartet Puzzling and NNI Operation

kalign

Global and progressive multiple sequence alignment

lagan

LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA

last

Genome-scale comparison of biological sequences

mafft

Multiple sequence alignments using a variety of algorithms

mammoth

MAtching Molecular Models Obtained from THeory

maq

Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences

maqview

GUI for sci-biology/maq, a short read mapping assembler

mauve

Multiple genome alignment with large-scale evolutionary events (GUI component)

mauvealigner

Multiple genome alignment with large-scale evolutionary events (aligner component)

mcl

A Markov Cluster Algorithm implementation

meme

The MEME/MAST system - Motif discovery and search

mira

Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina

mosaik

A reference-guided aligner for next-generation sequencing technologies

mothur

A suite of algorithms for ecological bioinformatics

mrbayes

Bayesian Inference of Phylogeny

mummer

A rapid whole genome aligner

muscle

Multiple sequence comparison by log-expectation

ncbi-tools

Development toolkit and applications for computational biology, including NCBI BLAST

ncbi-tools++

NCBI C++ Toolkit, including NCBI BLAST+

newick-utils

Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing)

njplot

A phylogenetic tree drawing program which supports tree rooting

pals

Pairwise Aligner for Long Sequences

paml

Phylogenetic Analysis by Maximum Likelihood

phrap

Phrap, swat, cross_match: Shotgun assembly and alignment utilities

phred

A base caller for Sanger DNA sequencing

phylip

PHYLIP - The PHYLogeny Inference Package

phyml

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

picard

Java-based command-line utilities that manipulate SAM files

piler

Analysis of repetitive DNA found in genome sequences

pilercr

Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

plink

Whole genome association analysis toolset

poa

Fast multiple sequence alignments using partial-order graphs

prank

Probabilistic Alignment Kit

primer3

Primer Design for PCR reactions

prints

A protein motif fingerprint database

probcons

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

prodigal

Prokaryotic Dynamic Programming Genefinding Algorithm

prosite

A protein families and domains database

psipred

Protein Secondary Structure Prediction

pysam

Python interface for the SAM/BAM sequence alignment and mapping format

qrna

Prototype ncRNA genefinder

raxml

A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees

readseq

Reads and writes nucleic/protein sequences in various formats.

rebase

A restriction enzyme database

recon

Automated de novo identification of repeat families from genomic sequences

repeatmasker

Screen DNA sequences for interspersed repeats and low complexity DNA

repeatmasker-libraries

A special version of RepBase used by RepeatMasker

rmblast

RepeatMasker compatible version of NCBI BLAST+

rnaview

Generates 2D displays of RNA/DNA secondary structures with tertiary interactions

samtools

Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments

seaview

A graphical multiple sequence alignment editor

shrimp

SHort Read Mapping Package

sibsim4

A rewrite and improvement upon sim4, a DNA-mRNA aligner

sim4

A program to align cDNA and genomic DNA

snpfile

A library and API for manipulating large SNP datasets

staden-bin

The Staden Package - Biological sequence handling and analysis

stride

Protein secondary structure assignment from atomic coordinates

t-coffee

A multiple sequence alignment package

tophat

A fast splice junction mapper for RNA-Seq reads

transfac

A database of eucaryotic transcription factors

tree-puzzle

Maximum likelihood analysis for nucleotide, amino acid, and two-state data

treeviewx

A phylogenetic tree viewer

trf

Tandem Repeats Finder

trnascan-se

tRNA detection in large-scale genome sequences

ucsc-genome-browser

The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath

unafold

Unified Nucleic Acid Folding and hybridization package

vaal

A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms

vcftools

Tools for working with VCF (Variant Call Format) files

velvet

A sequence assembler for very short reads

vienna-rna

RNA secondary structure prediction and comparison

wgs-assembler

A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG

wise

Intelligent algorithms for DNA searches

yass

Genomic similarity search with multiple transition constrained spaced seeds

aaindex

embassy-phylipnew

phred

abyss

embassy-signature

phylip

allpaths

embassy-structure

phyml

allpathslg

embassy-topo

picard

amap

embassy-vienna

piler

amos

emboss

pilercr

ApE

eugene

plink

arb

exonerate

poa

ariadne

express

prank

augustus

fasta

primer3

bamtools

fasttree

prints

beast-mcmc

finchtv

probcons

bedtools

foldingathome

prodigal

bfast

gatk

prosite

biogrep

GBrowse

psipred

bioperl

gibbs

pysam

bioperl-db

glimmer

qrna

bioperl-network

glimmerhmm

raxml

bioperl-run

gmap

readseq

biopython

goby

rebase

bioruby

goby-cpp

recon

biosql

hmmer

repeatmasker

blat

iedera

repeatmasker-libraries

blossoc

infernal

rmblast

bowtie

iqpnni

rnaview

bwa

kalign

samtools

cd-hit

lagan

seaview

clustal-omega

last

shrimp

clustalw

mafft

sibsim4

clustalw-mpi

mammoth

sim4

clustalx

maq

snpfile

consed

maqview

staden-bin

cufflinks

mauve

stride

cutg

mauvealigner

t-coffee

dialign-tx

mcl

tophat

diya

meme

transfac

elph

mira

tree-puzzle

embassy

mosaik

treeviewx

embassy-cbstools

mothur

trf

embassy-domainatrix

mrbayes

trnascan-se

embassy-domalign

mummer

ucsc-genome-browser

embassy-domsearch

muscle

unafold

embassy-emnu

ncbi-tools

vaal

embassy-esim4

ncbi-tools++

vcftools

embassy-hmmer

newick-utils

velvet

embassy-iprscan

njplot

vienna-rna

embassy-memenew

pals

wgs-assembler

embassy-mira

paml

wise

embassy-mse

phrap

yass