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aaindex
Amino acid indices and similarity matrices
abyss
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
align_to_scf
allpathslg
amap
amos
A Modular, Open-Source whole genome assembler
amos-short
ApE
apollo
arb
Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis
argo
argo-bin
ariadne
Protein sequences and profiles comparison
artemis
artemis-bin
Atlas2
augustus
Eukaryotic gene predictor
autoeditor
autoprime
A command line tool to generate primers for RT-PCR
autoprimeweb
A web frontend for AutoPrime
bambino
bambus
bamtools
BamView
barrnap
BBmap
beast-mcmc
Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences
bedtools
bfast
Blat-like Fast Accurate Search Tool
BG7
biogrep
Biogrep matchs large sets of patterns against biosequence dbs and is optimized for multithreading.
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 - Analysis run modules
biopieces
biopython
Biopython - Python modules for computational molecular biology
bioruby
An integrated environment for bioinformatics using the Ruby language
biosql
A generic bioinformatics relational database model
biskit
A Python platform for structural bioinformatics
blasr
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
boxshade-bin
brat
breakdancer
bwa
Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner
caftools
cap3-bin
cd-hit
cd-hit-auxtools
cdbfasta
ce
3-D protein structure comparison and alignment using the Combinatorial Extension (CE) method
cgview-bin
clover
Cis-eLement OVERrepresentation: Detection of functional DNA motifs
clustal-omega
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
cluster
Clustering software for microarray analysis
clview
codonw
Multivariate statistical analysis of codon and amino acid usage
conifer
consed
Consed: a genome sequence finishing program
consed-bin
consed2gap
CONTIGuator
cufflinks
cutadapt
cutg
Codon usage tables calculated from GenBank
cytoscape
dawg
DNA Assembly With Gaps: Phylogenetic aligner for sequence evolution simulation
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
emperor
ensembl-perl
Additional perl modules for bioperl that can be used to easily access the EnsEMBL database
ensembl-perl-compara
Additional perl modules for bioperl that can be used to easily access the EnsEMBL database
EpiGrass
erpin
Easy RNA Profile IdentificatioN, an RNA motif search program
est2uni
estscan
eugene
Eukaryotic gene predictor
eval
exonerate
exonerate is a generic tool for pairwise sequence comparison
express
fahmon
wxGTK monitor for the folding@home client
fasta
FASTA is a DNA and Protein sequence alignment software package
fastdnaml
Maximum likelihood phylogenetic tree builder for DNA sequences
fastqc
fasttree
Fast inference of approximately-maximum-likelihood phylogenetic trees
fastx_toolkit
finchtv
A cross-platform graphical viewer for chromatogram files.
FLASH
flexbar
flower
flowsim
foldingathome
Folding@Home is a distributed computing project for protein folding.
foldingathome-tools
foldx-bin
A force field for energy calculations in proteins
freebayes
fsa
Gambit
gap2caf
gatk
gbench
gbrowse
The generic genome browser provides a display of genomic annotations on interactive web pages
genepop
Population genetics analysis
generecon
Generecon performs linkage disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain Monte Carlo methods.
genomeview-bin
genseed
gibbs
The Gibbs Motif Sampler identifies 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
gnaural
A programmable binaural-beat generator, implementing the principle of binaural beats as described in the October 1973 Scientific American article "Auditory Beats in the Brain" (Gerald Oster).
goby
goby-cpp
grappa
Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
hmmer
Sequence analysis using profile hidden Markov models
hydra-sv
iedera
igv
IMAGE
imagej
infernal
Inference of RNA alignments
inGAP-bin
iqpnni
Important Quartet Puzzling and NNI Operation
jalview
A multiple DNA sequence alignment editor
jtreeview
Java TreeView renders gene expression data into several interactive views.
kalign
Global and progressive multiple sequence alignment
khmer
lagan
LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA
last
Genome-scale comparison of biological sequences
lastz
libgtextutils
lucy
mafft
Multiple sequence alignments using a variety of algorithms
MagicViewer
MAKER
mammoth
MAtching Molecular Models Obtained from THeory
manatee-igs
manatee-jcvi
mapview-bin
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
MaSuRCA
mauve
Multiple genome alignment with large-scale evolutionary events (GUI component)
mauvealigner
Multiple genome alignment with large-scale evolutionary events (aligner component)
mavid
Multiple alignment of large DNA sequences
mcl
meme
The MEME/MAST system - Motif discovery and search
merlin
Statistical analysis of gene flow in pedigrees
MeV
mgblast
microbiomeutil
mira
Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina
miranda
An algorithm for finding genomic targets for microRNAs
mne-python
mosaik
A reference-guided aligner for next-generation sequencing technologies
mothur
A suite of algorithms for ecological bioinformatics
mrbayes
Bayesian Inference of Phylogeny
mreps
Identification of serial/tandem repeats in DNA sequences
mrfast
mrsfast
msatfinder
mummer
A rapid whole genome aligner
muscle
Multiple sequence comparison by log-expectation
ncbi-blast+
ncbi-tools
Development toolkit and applications for computational biology, including NCBI BLAST
ncbi-tools++
NCBI C++ Toolkit, including NCBI BLAST+
nesoni
newick-utils
NGSTools
ngsview
ngs_backbone
njplot
A phylogenetic tree drawing program which supports tree rooting
nrcl
OBO-Edit
ONTO-PERL
pals
Pairwise Aligner for Long Sequences
paml
Phylogenetic Analysis by Maximum Likelihood
pandaseq
perlprimer
GUI application written in Perl to design primers for standard PCR, bisulphite PCR and Real-time PCR
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
Estimation of large phylogenies by maximum likelihood
picard
piler
Analysis of repetitive DNA found in genome sequences
pilercr
Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
pileup
plink
Whole genome association analysis toolset
poa
Fast multiple sequence alignments using partial-order graphs
prank
Probabilistic Alignment Kit
primer3
Design primers for PCR reactions.
prints
A protein motif fingerprint database
probalign
Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments
probcons
Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
proda
Multiple alignment of protein sequences with repeated and shuffled elements
prodigal
profphd
prosite
A protein families and domains database
psipred
Protein Secondary Structure Prediction
psx
psychopy
pybrain
pynast
pysam
pysurfer
qiime
qrna
Prototype ncRNA genefinder
quast
quicktree
Rapid reconstruction of phylogenies by the Neighbor-Joining method
RADtools
raxml
A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
Ray
readseq
Reads and writes nucleic/protein sequences in various formats.
rebase
A restriction enzyme database
recon
repbase
A database of repetetive genetic elements in various organisms.
repeatmasker
Screen DNA sequences for interspersed repeats and low complexity DNA
repeatmasker-libraries
A special version of RepBase used by RepeatMasker
rmblast
rnaplex
RNA-RNA interaction search
rnaview
Generates 2D displays of RNA/DNA secondary structures with tertiary interactions
roche454ace2caf
ruffus
samstat
samtools
SAM (Sequence Alignment/Map), a format for storing large nucleotide sequence alignments
sap
Pairwise protein structure alignment via double dynamic programming
sbagen
scaffold_builder
scan_for_matches
sclust
screed
scythe
seaview
A graphical multiple sequence alignment editor
seqan
seqclean
sequin
A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases
sff_dump
sga
shrimp
SHort Read Mapping Package
sibsim4
A rewrite and improvement upon sim4, a DNA-mRNA aligner
sickle
signalp
Prediction of signal peptide cleavage sites in amino acid sequences
sim4
A program to align cDNA and genomic DNA
skewer-bin
smalt-bin
snpfile
A library and API for manipulating large SNP datasets
SolexaQA
sombrero
sra_sdk
ssaha2-bin
stacks
staden
stride
A program for protein secondary structure assignment from atomic coordinates.
structure
surfaceracer
Calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules
swissknife
symap
t-coffee
A multiple sequence alignment package
tablet
tablet-bin
tclust
tgi-tools
The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx
tgicl
tigr-assembler
A whole-genome shotgun assembler from TIGR
tigr-foundation-libs
tmhmm
Prediction of transmembrane helices in proteins
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
trim_galore
trnascan-se
tRNA detection in large-scale genome sequences
twinscan
TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipeline
uchime
uclust-bin
ucsc-genome-browser
The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath
ugene
unafold
update-blastdb
vaal
A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms
VarScan
vcftools
velvet
A sequence assembler for very short reads
velvetk
VelvetOptimiser
vienna-rna
The Vienna RNA Package - RNA secondary structure prediction and comparison
wcd
wgs-assembler
Whole-genome shotgun assembler based on the Celera Assembler
wise
Intelligent algorithms for DNA searches
YASRA
yass
zmsort