Browse sci-biology in overlay gentoo
aaindex
Amino acid indices and similarity matricesabyss
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembleraugustus
Eukaryotic gene predictorbfast
Blat-like Fast Accurate Search Toolbioperl
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 biologybiosql
A generic bioinformatics relational database modelblat
The BLAST-Like Alignment Tool, a fast genomic sequence alignerbowtie
An ultrafast memory-efficient short read alignerbwa
Burrows-Wheeler Alignment Tool, a fast short genomic sequence alignerclustalw
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 programcutg
Codon usage tables calculated from GenBankdialign-tx
Greedy and progressive approaches for segment-based multiple sequence alignmentelph
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-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
exonerate is a generic tool for pairwise sequence comparisonfasta
FASTA is a DNA and Protein sequence alignment software packagefasttree
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.glimmer
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 Sequenceshmmer
Sequence analysis using profile hidden Markov modelsinfernal
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 DNAmafft
Multiple sequence alignments using a variety of algorithmsmaq
Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequencesmaqview
GUI for sci-biology/maq, a short read mapping assemblermosaik
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-expectationpals
Pairwise Aligner for Long Sequencespaml
Phylogenetic Analysis by Maximum Likelihoodphylip
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 databaseprobcons
Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequencesprosite
A protein families and domains databaseqrna
Prototype ncRNA genefinderraxml
A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Treesrebase
A restriction enzyme databasernaview
Generates 2D displays of RNA/DNA secondary structures with tertiary interactionssamtools
SAM (Sequence Alignment/Map), a format for storing large nucleotide sequence alignmentsseaview
A graphical multiple sequence alignment editorsibsim4
A rewrite and improvement upon sim4, a DNA-mRNA alignersim4
A program to align cDNA and genomic DNAstride
A program for protein secondary structure assignment from atomic coordinates.t-coffee
A multiple sequence alignment packagetree-puzzle
Maximum likelihood analysis for nucleotide, amino acid, and two-state data.treeviewx
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 GoldenPathvelvet
A sequence assembler for very short readswise
Intelligent algorithms for DNA searches
