Browse sci-biology
aaindex
Amino acid indices and similarity matricesabyss
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assemblerallpaths
De novo assembly of whole-genome shotgun microreadsamos
A Modular, Open-Source whole genome assemblerarb
Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysisariadne
Protein sequences and profiles comparisonaugustus
Eukaryotic gene predictorautoprime
A command line tool to generate primers for RT-PCRautoprimeweb
A web frontend for AutoPrimebeast-mcmc
Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequencesbfast
Blat-like Fast Accurate Search Toolbiogrep
Biogrep matchs large sets of patterns against biosequence dbs and is optimized for multithreading.bioperl
Perl tools for bioinformatics - Core modulesbioperl-db
Perl tools for bioinformatics - Perl API that accesses the BioSQL schemabioperl-network
Perl tools for bioinformatics - Analysis of protein-protein interaction networksbioperl-run
Perl tools for bioinformatics - Analysis run modulesbiopython
Biopython - Python modules for computational molecular biologybioruby
An integrated environment for bioinformatics using the Ruby languagebiosql
A generic bioinformatics relational database modelbiskit
A Python platform for structural bioinformaticsblat
The BLAST-Like Alignment Tool, a fast genomic sequence alignerblossoc
A linkage disequilibrium association mapping toolbowtie
An ultrafast memory-efficient short read alignerbwa
Burrows-Wheeler Alignment Tool, a fast short genomic sequence alignerce
3-D protein structure comparison and alignment using the Combinatorial Extension (CE) methodclover
Cis-eLement OVERrepresentation: Detection of functional DNA motifsclustalw
General purpose multiple alignment program for DNA and proteinsclustalw-mpi
A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithmclustalx
Graphical interface for the ClustalW multiple alignment programcluster
Clustering software for microarray analysiscodonw
Multivariate statistical analysis of codon and amino acid usageconsed
Consed: a genome sequence finishing programcutg
Codon usage tables calculated from GenBankdawg
DNA Assembly With Gaps: Phylogenetic aligner for sequence evolution simulationdialign-tx
Greedy and progressive approaches for segment-based multiple sequence alignmentdiya
Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotationelph
Estimated Locations of Pattern Hits - Motif finder programembassy
A meta-package for installing all EMBASSY packages (EMBOSS add-ons)embassy-cbstools
EMBOSS wrappers for applications from the CBS groupembassy-domainatrix
Protein domain analysis add-on package for EMBOSSembassy-domalign
Protein domain alignment add-on package for EMBOSSembassy-domsearch
Protein domain search add-on package for EMBOSSembassy-emnu
EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applicationsembassy-esim4
EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNAembassy-hmmer
EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMsembassy-iprscan
InterProScan motif detection add-on package for EMBOSSembassy-memenew
EMBOSS wrappers for MEME - Multiple Em for Motif Elicitationembassy-mira
Fragment assembly add-on package for EMBOSSembassy-mse
EMBOSS integrated version of MSE - Multiple Sequence Screen Editorembassy-phylipnew
EMBOSS integrated version of PHYLIP - The Phylogeny Inference Packageembassy-signature
Protein signature add-on package for EMBOSSembassy-structure
Protein structure add-on package for EMBOSSembassy-topo
EMBOSS integrated version of TOPO - Transmembrane protein displayembassy-vienna
EMBOSS integrated version of the Vienna RNA package - RNA foldingemboss
The European Molecular Biology Open Software Suite - A sequence analysis packageensembl-perl
Additional perl modules for bioperl that can be used to easily access the EnsEMBL databaseensembl-perl-compara
Additional perl modules for bioperl that can be used to easily access the EnsEMBL databaseerpin
Easy RNA Profile IdentificatioN, an RNA motif search programeugene
Eukaryotic gene predictorexonerate
exonerate is a generic tool for pairwise sequence comparisonfahmon
wxGTK monitor for the folding@home clientfasta
FASTA is a DNA and Protein sequence alignment software packagefastdnaml
Maximum likelihood phylogenetic tree builder for DNA sequencesfasttree
Fast inference of approximately-maximum-likelihood phylogenetic treesfinchtv
A cross-platform graphical viewer for chromatogram files.foldingathome
Folding@Home is a distributed computing project for protein folding.foldx-bin
A force field for energy calculations in proteinsgbrowse
The generic genome browser provides a display of genomic annotations on interactive web pagesgenepop
Population genetics analysisgenerecon
Generecon performs linkage disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain Monte Carlo methods.gibbs
The Gibbs Motif Sampler identifies motifs, conserved regions, in DNA or protein sequencesglimmer
An HMM-based microbial gene finding system from TIGRglimmerhmm
An eukaryotic gene finding system from TIGRgmap
A Genomic Mapping and Alignment Program for mRNA and EST Sequencesgnaural
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).grappa
Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithmshmmer
Sequence analysis using profile hidden Markov modelsinfernal
Inference of RNA alignmentsiqpnni
Important Quartet Puzzling and NNI Operationjalview
A multiple DNA sequence alignment editorjtreeview
Java TreeView renders gene expression data into several interactive views.kalign
Global and progressive multiple sequence alignmentlagan
LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNAlast
Genome-scale comparison of biological sequencesmafft
Multiple sequence alignments using a variety of algorithmsmammoth
MAtching Molecular Models Obtained from THeorymaq
Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequencesmaqview
GUI for sci-biology/maq, a short read mapping assemblermauve
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 sequencesmeme
The MEME/MAST system - Motif discovery and searchmerlin
Statistical analysis of gene flow in pedigreesmira
Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illuminamiranda
An algorithm for finding genomic targets for microRNAsmmult
MAtching Molecular Models Obtained from THeorymosaik
A reference-guided aligner for next-generation sequencing technologiesmothur
A suite of algorithms for ecological bioinformaticsmpiblast
An MPI implementation of NCBI BLASTmrbayes
Bayesian Inference of Phylogenymreps
Identification of serial/tandem repeats in DNA sequencesmummer
A rapid whole genome alignermuscle
Multiple sequence comparison by log-expectationncbi-tools
Development toolkit and applications for computational biology, including NCBI BLASTncbi-tools++
NCBI C++ Toolkit, including NCBI BLAST+newbler
Roche 454 pyrosequencing assemblernjplot
A phylogenetic tree drawing program which supports tree rootingpals
Pairwise Aligner for Long Sequencespaml
Phylogenetic Analysis by Maximum Likelihoodperlprimer
GUI application written in Perl to design primers for standard PCR, bisulphite PCR and Real-time PCRphrap
Phrap, swat, cross_match: Shotgun assembly and alignment utilitiesphred
A base caller for Sanger DNA sequencingphylip
PHYLIP - The PHYLogeny Inference Packagephyml
Estimation of large phylogenies by maximum likelihoodpiler
Analysis of repetitive DNA found in genome sequencespilercr
Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)plink
Whole genome association analysis toolsetpoa
Fast multiple sequence alignments using partial-order graphsprank
Probabilistic Alignment Kitprimer3
Design primers for PCR reactions.prints
A protein motif fingerprint databaseprobalign
Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignmentsprobcons
Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequencesproda
Multiple alignment of protein sequences with repeated and shuffled elementsprosite
A protein families and domains databasepsipred
Protein Secondary Structure Predictionqrna
Prototype ncRNA genefinderquicktree
Rapid reconstruction of phylogenies by the Neighbor-Joining methodraxml
A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Treesreadseq
Reads and writes nucleic/protein sequences in various formats.rebase
A restriction enzyme databaserepbase
A database of repetetive genetic elements in various organisms.repeatmasker
Screen DNA sequences for interspersed repeats and low complexity DNArepeatmasker-libraries
A special version of RepBase used by RepeatMaskerrnaplex
RNA-RNA interaction searchrnaview
Generates 2D displays of RNA/DNA secondary structures with tertiary interactionssamtools
SAM (Sequence Alignment/Map), a format for storing large nucleotide sequence alignmentssap
Pairwise protein structure alignment via double dynamic programmingseaview
A graphical multiple sequence alignment editorsequin
A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databasesshrimp
SHort Read Mapping Packagesibsim4
A rewrite and improvement upon sim4, a DNA-mRNA alignersignalp
Prediction of signal peptide cleavage sites in amino acid sequencessim4
A program to align cDNA and genomic DNAsnpfile
A library and API for manipulating large SNP datasetsstaden-bin
The Staden Package - Biological sequence handling and analysisstride
A program for protein secondary structure assignment from atomic coordinates.surfaceracer
Calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromoleculest-coffee
A multiple sequence alignment packagetgi-tools
The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psxtigr-assembler
A whole-genome shotgun assembler from TIGRTMalign
Computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrixtmhmm
Prediction of transmembrane helices in proteinstophat
A fast splice junction mapper for RNA-Seq readstransfac
A database of eucaryotic transcription factorstree-puzzle
Maximum likelihood analysis for nucleotide, amino acid, and two-state data.treeviewx
A phylogenetic tree viewertrnascan-se
tRNA detection in large-scale genome sequencestwinscan
TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipelineucsc-genome-browser
The UCSC genome browser suite, also known as Jim Kent's library and GoldenPathvaal
A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphismsvelvet
A sequence assembler for very short readsvienna-rna
The Vienna RNA Package - RNA secondary structure prediction and comparisonwgs-assembler
Whole-genome shotgun assembler based on the Celera Assemblerwise
Intelligent algorithms for DNA searches
