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

arcs

assembly-stats

augustus

Eukaryotic gene predictor

bam-readcount

bambus

bamql

bamstats

bamtools

barrnap

BBmap

bcftools

beagle

beaglecall

bedops

bedtools

behaviopy

betse

bfast

Blat-like Fast Accurate Search Tool

bids-cli

bids-schema

bidsschematools

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

blat

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

bowtie

An ultrafast memory-efficient short read aligner

BRAKER

BRANCH

brat

brat_bw

brat_nova

bru2nii

bruker2nifti

btl_bloomfilter

bwa

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

bx-python

cast-bin

CAT

cd-hit

cdbfasta

cellblender

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

cmdock

cnrun

codonw

conform-gt

coral

cross_genome

cutg

Codon usage tables calculated from GenBank

dargcc_bidsdata

dcm2niix

dcmstack

deeptools

deeptools-intervals

dialign-tx

Greedy and progressive approaches for segment-based multiple sequence alignment

dialign2

diamond

dipy

drlfom_bidsdata

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

epga

erpin

eugene

Eukaryotic gene predictor

exonerate

exonerate is a generic tool for pairwise sequence comparison

exonerate-gff3

express

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.

freebayes

fsa

fsl

GAL

geneathome

genepop

genomeview-bin

germline

gffcompare

gffread

gffutils

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

hexamer

hisat2

hmmer

Sequence analysis using profile hidden Markov models

HTSeq

idba

iedera

IMAGE

imagej

infernal

Inference of RNA alignments

iqpnni

Important Quartet Puzzling and NNI Operation

irsabi_bidsdata

irsabi_brudata

jannovar-bin

jellyfish

jtreeview-bin

KaKs_Calculator

kalign

Global and progressive multiple sequence alignment

kallisto

karect

KING

lagan

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

lastz

lemur-brain-atlas

libBigWig

libgtextutils

lighter

LINKS

longstitch

lucy

lumpy-sv

mafft

Multiple sequence alignments using a variety of algorithms

mappy

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

mcell

mcl

megahit

merlin

Statistical analysis of gene flow in pedigrees

MeV

mfold_util

minced

minimap2

mip-scaffolder

miranda

An algorithm for finding genomic targets for microRNAs

mmseqs2

MochiView

mosaik

A reference-guided aligner for next-generation sequencing technologies

mothur

A suite of algorithms for ecological bioinformatics

mouse-brain-templates

mrbayes

Bayesian Inference of Phylogeny

mreps

mrfast

msautil

mummer

A rapid whole genome aligner

muscle

Multiple sequence comparison by log-expectation

MuSeqBox

nanopolish

ncbi-vdb

neuroconv

newick-utils

nextclip

ngs

NGSEPcore

NGSEPcore-bin

nilearn

nitime

nrcl

ntCard

nvcz_data

nvcz_preprocessed

nxtrim

ONTO-PERL

open-ephys-gui

opfvta_bidsdata

opfvta_brudata

pairagon

pals

Pairwise Aligner for Long Sequences

paml

Phylogenetic Analysis by Maximum Likelihood

ParaAT

parafly

pbbam

pbcopper

perga

perlprimer

phylip

PHYLIP - The PHYLogeny Inference Package

phyml

Estimation of large phylogenies by maximum likelihood

piler

Analysis of repetitive DNA found in genome sequences

pilercr

Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

pileup

plamri_brudata

plink

Whole genome association analysis toolset

poa

Fast multiple sequence alignments using partial-order graphs

portrait

prank

Probabilistic Alignment Kit

primer3

Design primers for PCR reactions.

prinseq-lite

prints

A protein motif fingerprint database

probcons

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

proda

prodigal

profphd

prosite

A protein families and domains database

psx

pybedtools

pyfaidx

pysam

qrna

Prototype ncRNA genefinder

quicktree

RAILS

rat-brain-templates

raxml

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

Rcorrector

rebase

A restriction enzyme database

recon

rnaplex

rnaview

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

roiextractors

sabre

samri

samri_bidsdata

samri_bindata

samstat

samtools

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

scan_for_matches

scythe

seaview

A graphical multiple sequence alignment editor

SEECER

seqan

seqtk

seqtools

sff_dump

sga

sibsim4

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

sickle

sim4

A program to align cDNA and genomic DNA

skewer-bin

smalt

smalt-bin

snap

SnpEff

snpomatic

SolexaQA

SPAdes

spm

sra-tools

ssaha2-bin

SSAKE

stacks

STAR

stride

A program for protein secondary structure assignment from atomic coordinates.

stringtie

structure

subread

swissknife

t-coffee

A multiple sequence alignment package

tabixpp

tagdust

tigmint

tigr-foundation-libs

TransDecoder

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

trinityrnaseq

trnascan-se

tRNA detection in large-scale genome sequences

twinscan

uchime

ucsc-genome-browser

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

ugene

unafold

update-blastdb

vague-bin

VarScan

VarScan-bin

vcflib

vcftools

velvet

A sequence assembler for very short reads

VelvetOptimiser

verifyBamID

vt

wgs_tools

wise

Intelligent algorithms for DNA searches

yaha

YASRA

yass

zmap

zmsort

ztau_bidsdata

aaindex

Fastaq

pbbam

abacas

fastdnaml

pbcopper

ABI-connectivity-data

fastqc

perga

ABI-expression-data

fasttree

perlprimer

abyss

fastx_toolkit

phylip

act-bin

ffindex

phyml

afni

finchtv

piler

aghermann

FLASH

pilercr

AlignGraph

flexbar

pileup

align_to_scf

flowsim

plamri_brudata

amap

foldingathome

plink

ANGLE-bin

freebayes

poa

angsd

fsa

portrait

ants

fsl

prank

arcs

GAL

primer3

assembly-stats

geneathome

prinseq-lite

augustus

genepop

prints

bam-readcount

genomeview-bin

probcons

bambus

germline

proda

bamql

gffcompare

prodigal

bamstats

gffread

profphd

bamtools

gffutils

prosite

barrnap

glean

psx

BBmap

glimmer

pybedtools

bcftools

glimmerhmm

pyfaidx

beagle

gmap

pysam

beaglecall

gnaural

qrna

bedops

grabix

quicktree

bedtools

graf-bin

RAILS

behaviopy

grappa

rat-brain-templates

betse

hexamer

raxml

bfast

hisat2

Rcorrector

bids-cli

hmmer

rebase

bids-schema

HTSeq

recon

bidsschematools

idba

rnaplex

biobambam2

iedera

rnaview

biogrep

IMAGE

roiextractors

biopandas

imagej

sabre

bioperl

infernal

samri

bioperl-db

iqpnni

samri_bidsdata

bioperl-network

irsabi_bidsdata

samri_bindata

bioperl-run

irsabi_brudata

samstat

biopython

jannovar-bin

samtools

biosql

jellyfish

scan_for_matches

bismark

jtreeview-bin

scythe

blat

KaKs_Calculator

seaview

bowtie

kalign

SEECER

BRAKER

kallisto

seqan

BRANCH

karect

seqtk

brat

KING

seqtools

brat_bw

lagan

sff_dump

brat_nova

lastz

sga

bru2nii

lemur-brain-atlas

sibsim4

bruker2nifti

libBigWig

sickle

btl_bloomfilter

libgtextutils

sim4

bwa

lighter

skewer-bin

bx-python

LINKS

smalt

cast-bin

longstitch

smalt-bin

CAT

lucy

snap

cd-hit

lumpy-sv

SnpEff

cdbfasta

mafft

snpomatic

cellblender

mappy

SolexaQA

clustal-omega

maq

SPAdes

clustalw

maqview

spm

clustalw-mpi

MaSuRCA

sra-tools

clustalx

mcell

ssaha2-bin

cluster

mcl

SSAKE

clview

megahit

stacks

cmdock

merlin

STAR

cnrun

MeV

stride

codonw

mfold_util

stringtie

conform-gt

minced

structure

coral

minimap2

subread

cross_genome

mip-scaffolder

swissknife

cutg

miranda

t-coffee

dargcc_bidsdata

mmseqs2

tabixpp

dcm2niix

MochiView

tagdust

dcmstack

mosaik

tigmint

deeptools

mothur

tigr-foundation-libs

deeptools-intervals

mouse-brain-templates

TransDecoder

dialign-tx

mrbayes

tree-puzzle

dialign2

mreps

treeviewx

diamond

mrfast

trf

dipy

msautil

trf-bin

drlfom_bidsdata

mummer

trimmomatic

edena

muscle

trinityrnaseq

elph

MuSeqBox

trnascan-se

embassy

nanopolish

twinscan

embassy-cbstools

ncbi-vdb

uchime

embassy-clustalomega

neuroconv

ucsc-genome-browser

embassy-domainatrix

newick-utils

ugene

embassy-domalign

nextclip

unafold

embassy-domsearch

ngs

update-blastdb

embassy-emnu

NGSEPcore

vague-bin

embassy-esim4

NGSEPcore-bin

VarScan

embassy-hmmer

nilearn

VarScan-bin

embassy-iprscan

nitime

vcflib

embassy-mse

nrcl

vcftools

embassy-phylipnew

ntCard

velvet

embassy-signature

nvcz_data

VelvetOptimiser

embassy-structure

nvcz_preprocessed

verifyBamID

embassy-topo

nxtrim

vt

embassy-vienna

ONTO-PERL

wgs_tools

emboss

open-ephys-gui

wise

epga

opfvta_bidsdata

yaha

erpin

opfvta_brudata

YASRA

eugene

pairagon

yass

exonerate

pals

zmap

exonerate-gff3

paml

zmsort

express

ParaAT

ztau_bidsdata

fasta

parafly