aaindex

Amino acid indices and similarity matrices

abacas

ABI-connectivity-data

ABI-expression-data

abyss

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

act-bin

afni

aghermann

AlignGraph

align_to_scf

amap

ANGLE-bin

angsd

ants

ApE

apollo

arachne

argo-bin

assembly-stats

augustus

Eukaryotic gene predictor

autoeditor

bam-readcount

bambino

bambus

bamql

bamstats

bamtools

barnacle

barrnap

BBmap

bcftools

beagle

beaglecall

bedops

bedtools

behaviopy

betse

betsee

bfast

Blat-like Fast Accurate Search Tool

BG7

biobambam2

biogrep

biopandas

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

biopython

Biopython - Python modules for computational molecular biology

biosql

A generic bioinformatics relational database model

bismark

blasr

BlastToSam

blat

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

blue

bowtie

An ultrafast memory-efficient short read aligner

BRAKER

BRANCH

brat

brat_bw

brat_nova

breakdancer

bru2nii

bruker2nifti

bwa

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

bx-python

caftools

canu

cast-bin

CAT

cd-hit

cd-hit-auxtools

cdbfasta

cegma

cellblender

cg-cat

cgview-bin

chiron

clover

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

clview

cnrun

codonw

conform-gt

conifer

conrad

consed

Consed: a genome sequence finishing program

coral

cortex_var

cramtools

cross_genome

cutadapt

cutg

Codon usage tables calculated from GenBank

dargcc_bidsdata

dawg

dcm2niix

dcmstack

deeptools

dialign-tx

Greedy and progressive approaches for segment-based multiple sequence alignment

dialign2

diamond

dipy

diya

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

dna2pep

drlfom_bidsdata

EBARDenovo

edena

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-clustalomega

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-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

ensembl-tools

ePCR

epga

EpiGrass

erne

erpin

est2assembly

ESTate

estscan

eugene

Eukaryotic gene predictor

eval

exonerate

exonerate is a generic tool for pairwise sequence comparison

exonerate-gff3

express

fah-control

fah-viewer

fahmon

fasta

FASTA is a DNA and Protein sequence alignment software package

Fastaq

fastdnaml

Maximum likelihood phylogenetic tree builder for DNA sequences

fastqc

fasttree

Fast inference of approximately-maximum-likelihood phylogenetic trees

fastx_toolkit

ffindex

finchtv

A cross-platform graphical viewer for chromatogram files.

FLASH

flexbar

flowsim

foldingathome

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

foldingathome-tools

freebayes

fsa

fsl

GAL

gap2caf

gatk

gbrowse

The generic genome browser provides a display of genomic annotations on interactive web pages

gemini

geneid

genepop

generecon

genomeview-bin

germline

gffcompare

gffread

gfftools

gffutils

gibbs

The Gibbs Motif Sampler identifies motifs, conserved regions, in DNA or protein sequences

glean

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

grabix

graf-bin

grappa

Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

grass

hexamer

hisat2

hmmer

Sequence analysis using profile hidden Markov models

hts-python

HTSeq

hydra-sv

ICC

idba

iedera

igv

IMAGE

imagej

infernal

Inference of RNA alignments

InterMine

iqpnni

Important Quartet Puzzling and NNI Operation

irsabi_bidsdata

irsabi_brudata

jannovar

jannovar-bin

jellyfish

jigsaw

jtreeview

jtreeview-bin

KaKs_Calculator

kalign

Global and progressive multiple sequence alignment

kallisto

karect

kat

khmer

KING

kmergenie

kraken

lagan

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

last

Genome-scale comparison of biological sequences

lastz

lemur-brain-atlas

libBigWig

libgtextutils

lighter

lucy

lumpy-sv

mafft

Multiple sequence alignments using a variety of algorithms

MagicViewer

maker

manatee-igs

manatee-jcvi

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

mavid

mcell

mcl

megahit

merlin

Statistical analysis of gene flow in pedigrees

MeV

mfold_util

mgblast

minced

mip-scaffolder

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

MochiView

MolBioLib

mosaik

A reference-guided aligner for next-generation sequencing technologies

mothur

A suite of algorithms for ecological bioinformatics

mouse-brain-atlases

mrbayes

Bayesian Inference of Phylogeny

mreps

mrfast

mRNAmarkup

mrsfast

msautil

mummer

A rapid whole genome aligner

muscle

Multiple sequence comparison by log-expectation

MuSeqBox

nanopolish

ncbi-blast+

ncbi-genome-download

ncbi-tools

Development toolkit and applications for computational biology, including NCBI BLAST

ncbi-tools++

newick-utils

nextclip

NGSEPcore

NGSEPcore-bin

NGSEPplugin

NGSEPplugin-bin

nilearn

nitime

njplot

A phylogenetic tree drawing program which supports tree rooting

nrcl

ntCard

nvcz_data

nwalign3

nxtrim

oases

OBO-Edit

ONTO-PERL

opfvta_bidsdata

opfvta_brudata

ORFcor

pairagon

pals

Pairwise Aligner for Long Sequences

paml

Phylogenetic Analysis by Maximum Likelihood

ParaAT

parafly

pbbam

perga

perlprimer

phrap

Phrap, swat, cross_match: Shotgun assembly and alignment utilities

phred

A base caller for Sanger DNA sequencing

phusion

phusion2

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

pilon-bin

plink

Whole genome association analysis toolset

plinkseq

poa

Fast multiple sequence alignments using partial-order graphs

polyphen

portrait

prank

Probabilistic Alignment Kit

primer3

Design primers for PCR reactions.

primerD

prinseq-lite

prints

A protein motif fingerprint database

probcons

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

proda

prodigal

profphd

prokka

proovread

prosite

A protein families and domains database

prot4EST

psipred

Protein Secondary Structure Prediction

psx

pvmsx

pybedtools

pyfaidx

pysam

pysamstats

qrna

Prototype ncRNA genefinder

quast

quicktree

quorum

RADtools

RAILS

rarecoal

rat-brain-atlases

raxml

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

Rcorrector

reaper

reapr

rebase

A restriction enzyme database

recon

repeatmasker

Screen DNA sequences for interspersed repeats and low complexity DNA

repeatmasker-libraries

A special version of RepBase used by RepeatMasker

reptile

rmblast

rnaplex

rnaview

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

roche454ace2caf

RSeQC

rtg-tools

ruffus

rum

sabre

sailfish

salmon

sambamba

samri

samri_bidsdata

samri_bindata

samstat

samtools

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

Scaffolder-evaluation

scaffold_builder

scan_for_matches

sclust

screed

scythe

seaview

A graphical multiple sequence alignment editor

SEECER

seqan

seqclean

seqtk

seqtools

seq_crumbs

sff_dump

sga

sgp2

Sibelia

sibsim4

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

sickle

signalp

sim4

A program to align cDNA and genomic DNA

skewer-bin

smalt

smalt-bin

snap

SnpEff

snphylo

snpomatic

SOAPdenovo2

SolexaQA

somatic-sniper

SPAdes

spm

sra_sdk

ssaha2-bin

SSAKE

stacks

staden

staden_doc

stampy-bin

STAR

StarORF

stride

A program for protein secondary structure assignment from atomic coordinates.

stringtie

structure

subread

swissknife

symap

t-coffee

A multiple sequence alignment package

tablet

tablet-bin

tagdust

tclust

tigmint

tigr-foundation-libs

tmhmm

trans-abyss

TransDecoder

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

trf-bin

trimmomatic

trim_galore

trinityrnaseq

Trinotate

trnascan-se

tRNA detection in large-scale genome sequences

trowel

twinscan

uchime

ucsc-genome-browser

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

unafold

update-blastdb

vague-bin

VarScan

VarScan-bin

vcflib

vcftools

velvet

A sequence assembler for very short reads

VelvetOptimiser

verifyBamID

vt

wcd

weblogo

wgs-assembler

Whole-genome shotgun assembler based on the Celera Assembler

wgs_tools

wise

Intelligent algorithms for DNA searches

yaha

YASRA

yass

zmap

zmsort

ztau_bidsdata

aaindex

FLASH

plinkseq

abacas

flexbar

poa

ABI-connectivity-data

flowsim

polyphen

ABI-expression-data

foldingathome

portrait

abyss

foldingathome-tools

prank

act-bin

freebayes

primer3

afni

fsa

primerD

aghermann

fsl

prinseq-lite

AlignGraph

GAL

prints

align_to_scf

gap2caf

probcons

amap

gatk

proda

ANGLE-bin

gbrowse

prodigal

angsd

gemini

profphd

ants

geneid

prokka

ApE

genepop

proovread

apollo

generecon

prosite

arachne

genomeview-bin

prot4EST

argo-bin

germline

psipred

assembly-stats

gffcompare

psx

augustus

gffread

pvmsx

autoeditor

gfftools

pybedtools

bam-readcount

gffutils

pyfaidx

bambino

gibbs

pysam

bambus

glean

pysamstats

bamql

glimmer

qrna

bamstats

glimmerhmm

quast

bamtools

gmap

quicktree

barnacle

gnaural

quorum

barrnap

grabix

RADtools

BBmap

graf-bin

RAILS

bcftools

grappa

rarecoal

beagle

grass

rat-brain-atlases

beaglecall

hexamer

raxml

bedops

hisat2

Rcorrector

bedtools

hmmer

reaper

behaviopy

hts-python

reapr

betse

HTSeq

rebase

betsee

hydra-sv

recon

bfast

ICC

repeatmasker

BG7

idba

repeatmasker-libraries

biobambam2

iedera

reptile

biogrep

igv

rmblast

biopandas

IMAGE

rnaplex

bioperl

imagej

rnaview

bioperl-db

infernal

roche454ace2caf

bioperl-network

InterMine

RSeQC

bioperl-run

iqpnni

rtg-tools

biopython

irsabi_bidsdata

ruffus

biosql

irsabi_brudata

rum

bismark

jannovar

sabre

blasr

jannovar-bin

sailfish

BlastToSam

jellyfish

salmon

blat

jigsaw

sambamba

blue

jtreeview

samri

bowtie

jtreeview-bin

samri_bidsdata

BRAKER

KaKs_Calculator

samri_bindata

BRANCH

kalign

samstat

brat

kallisto

samtools

brat_bw

karect

Scaffolder-evaluation

brat_nova

kat

scaffold_builder

breakdancer

khmer

scan_for_matches

bru2nii

KING

sclust

bruker2nifti

kmergenie

screed

bwa

kraken

scythe

bx-python

lagan

seaview

caftools

last

SEECER

canu

lastz

seqan

cast-bin

lemur-brain-atlas

seqclean

CAT

libBigWig

seqtk

cd-hit

libgtextutils

seqtools

cd-hit-auxtools

lighter

seq_crumbs

cdbfasta

lucy

sff_dump

cegma

lumpy-sv

sga

cellblender

mafft

sgp2

cg-cat

MagicViewer

Sibelia

cgview-bin

maker

sibsim4

chiron

manatee-igs

sickle

clover

manatee-jcvi

signalp

clustal-omega

maq

sim4

clustalw

maqview

skewer-bin

clustalw-mpi

MaSuRCA

smalt

clustalx

mavid

smalt-bin

cluster

mcell

snap

clview

mcl

SnpEff

cnrun

megahit

snphylo

codonw

merlin

snpomatic

conform-gt

MeV

SOAPdenovo2

conifer

mfold_util

SolexaQA

conrad

mgblast

somatic-sniper

consed

minced

SPAdes

coral

mip-scaffolder

spm

cortex_var

mira

sra_sdk

cramtools

miranda

ssaha2-bin

cross_genome

mne-python

SSAKE

cutadapt

MochiView

stacks

cutg

MolBioLib

staden

dargcc_bidsdata

mosaik

staden_doc

dawg

mothur

stampy-bin

dcm2niix

mouse-brain-atlases

STAR

dcmstack

mrbayes

StarORF

deeptools

mreps

stride

dialign-tx

mrfast

stringtie

dialign2

mRNAmarkup

structure

diamond

mrsfast

subread

dipy

msautil

swissknife

diya

mummer

symap

dna2pep

muscle

t-coffee

drlfom_bidsdata

MuSeqBox

tablet

EBARDenovo

nanopolish

tablet-bin

edena

ncbi-blast+

tagdust

elph

ncbi-genome-download

tclust

embassy

ncbi-tools

tigmint

embassy-cbstools

ncbi-tools++

tigr-foundation-libs

embassy-clustalomega

newick-utils

tmhmm

embassy-domainatrix

nextclip

trans-abyss

embassy-domalign

NGSEPcore

TransDecoder

embassy-domsearch

NGSEPcore-bin

transfac

embassy-emnu

NGSEPplugin

tree-puzzle

embassy-esim4

NGSEPplugin-bin

treeviewx

embassy-hmmer

nilearn

trf

embassy-iprscan

nitime

trf-bin

embassy-mse

njplot

trimmomatic

embassy-phylipnew

nrcl

trim_galore

embassy-signature

ntCard

trinityrnaseq

embassy-structure

nvcz_data

Trinotate

embassy-topo

nwalign3

trnascan-se

embassy-vienna

nxtrim

trowel

emboss

oases

twinscan

ensembl-tools

OBO-Edit

uchime

ePCR

ONTO-PERL

ucsc-genome-browser

epga

opfvta_bidsdata

unafold

EpiGrass

opfvta_brudata

update-blastdb

erne

ORFcor

vague-bin

erpin

pairagon

VarScan

est2assembly

pals

VarScan-bin

ESTate

paml

vcflib

estscan

ParaAT

vcftools

eugene

parafly

velvet

eval

pbbam

VelvetOptimiser

exonerate

perga

verifyBamID

exonerate-gff3

perlprimer

vt

express

phrap

wcd

fah-control

phred

weblogo

fah-viewer

phusion

wgs-assembler

fahmon

phusion2

wgs_tools

fasta

phylip

wise

Fastaq

phyml

yaha

fastdnaml

picard

YASRA

fastqc

piler

yass

fasttree

pilercr

zmap

fastx_toolkit

pileup

zmsort

ffindex

pilon-bin

ztau_bidsdata

finchtv

plink