Категория 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 microreadsallpathslg
De novo assembly of whole-genome shotgun microreadsamap
Protein multiple-alignment-based sequence annealingamos
A Modular, Open-Source whole genome assemblerApE
ApE - A Plasmid Editorarb
Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysisariadne
Protein sequences and profiles comparisonaugustus
Eukaryotic gene predictorbamtools
A programmer's API and an end-user's toolkit for handling BAM filesbeast-mcmc
Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequencesbedtools
Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formatsbfast
Blat-like Fast Accurate Search Toolbiogrep
Multithreading application for matching large sets of patterns against biosequence dbs.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
Python modules for computational molecular biologybioruby
An integrated environment for bioinformatics using the Ruby languagebiosql
A generic bioinformatics relational database modelblat
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 alignercd-hit
Clustering Database at High Identity with Toleranceclustal-omega
Scalable multiple alignment of protein sequencesclustalw
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 programconsed
Consed: a genome sequence finishing programcufflinks
Transcript assembly, differential expression, and differential regulation for RNA-Seqcutg
Codon usage tables calculated from GenBankdialign-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 packageeugene
Eukaryotic gene predictorexonerate
Generic tool for pairwise sequence comparisonexpress
Streaming RNA-Seq Analysisfasta
FASTA is a DNA and Protein sequence alignment software packagefasttree
Fast inference of approximately-maximum-likelihood phylogenetic treesfinchtv
Graphical viewer for chromatogram filesfoldingathome
Folding@Home is a distributed computing project for protein folding.gatk
The Genome Analysis ToolkitGBrowse
Generic Model Organism Database Project - The Generic Genome Browsergibbs
Identify 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 Sequencesgoby
A DNA sequencing data management frameworkgoby-cpp
A DNA sequencing data management framework - C/C++ APIhmmer
Sequence analysis using profile hidden Markov modelsiedera
A subset seed design tool for DNA sequence alignmentinfernal
Inference of RNA alignmentsiqpnni
Important Quartet Puzzling and NNI Operationkalign
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)mcl
A Markov Cluster Algorithm implementationmeme
The MEME/MAST system - Motif discovery and searchmira
Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illuminamosaik
A reference-guided aligner for next-generation sequencing technologiesmothur
A suite of algorithms for ecological bioinformaticsmrbayes
Bayesian Inference of Phylogenymummer
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+newick-utils
Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing)njplot
A phylogenetic tree drawing program which supports tree rootingpals
Pairwise Aligner for Long Sequencespaml
Phylogenetic Analysis by Maximum Likelihoodphrap
Phrap, swat, cross_match: Shotgun assembly and alignment utilitiesphred
A base caller for Sanger DNA sequencingphylip
PHYLIP - The PHYLogeny Inference Packagephyml
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.picard
Java-based command-line utilities that manipulate SAM filespiler
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
Primer Design for PCR reactionsprints
A protein motif fingerprint databaseprobcons
Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequencesprodigal
Prokaryotic Dynamic Programming Genefinding Algorithmprosite
A protein families and domains databasepsipred
Protein Secondary Structure Predictionpysam
Python interface for the SAM/BAM sequence alignment and mapping formatqrna
Prototype ncRNA genefinderraxml
A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Treesreadseq
Reads and writes nucleic/protein sequences in various formats.rebase
A restriction enzyme databaserecon
Automated de novo identification of repeat families from genomic sequencesrepeatmasker
Screen DNA sequences for interspersed repeats and low complexity DNArepeatmasker-libraries
A special version of RepBase used by RepeatMaskerrmblast
RepeatMasker compatible version of NCBI BLAST+rnaview
Generates 2D displays of RNA/DNA secondary structures with tertiary interactionssamtools
Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignmentsseaview
A graphical multiple sequence alignment editorshrimp
SHort Read Mapping Packagesibsim4
A rewrite and improvement upon sim4, a DNA-mRNA alignersim4
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
Protein secondary structure assignment from atomic coordinatest-coffee
A multiple sequence alignment packagetophat
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 datatreeviewx
A phylogenetic tree viewertrnascan-se
tRNA detection in large-scale genome sequencesucsc-genome-browser
The UCSC genome browser suite, also known as Jim Kent's library and GoldenPathunafold
Unified Nucleic Acid Folding and hybridization packagevaal
A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphismsvcftools
Tools for working with VCF (Variant Call Format) filesvelvet
A sequence assembler for very short readsvienna-rna
RNA secondary structure prediction and comparisonwgs-assembler
A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOGwise
Intelligent algorithms for DNA searchesyass
Genomic similarity search with multiple transition constrained spaced seeds