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Amino acid indices and similarity matrices

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

De novo assembly of whole-genome shotgun microreads

A Modular, Open-Source whole genome assembler

Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis

Protein sequences and profiles comparison

Eukaryotic gene predictor

A command line tool to generate primers for RT-PCR

A web frontend for AutoPrime

Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences

Blat-like Fast Accurate Search Tool

Biogrep matchs large sets of patterns against biosequence dbs and is optimized for multithreading.

Perl tools for bioinformatics - Core modules

Perl tools for bioinformatics - Perl API that accesses the BioSQL schema

bioperl-network

Perl tools for bioinformatics - Analysis of protein-protein interaction networks

Perl tools for bioinformatics - Analysis run modules

Biopython - Python modules for computational molecular biology

An integrated environment for bioinformatics using the Ruby language

A generic bioinformatics relational database model

A Python platform for structural bioinformatics

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

A linkage disequilibrium association mapping tool

An ultrafast memory-efficient short read aligner

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

3-D protein structure comparison and alignment using the Combinatorial Extension (CE) method

Cis-eLement OVERrepresentation: Detection of functional DNA motifs

General purpose multiple alignment program for DNA and proteins

A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm

Graphical interface for the ClustalW multiple alignment program

Clustering software for microarray analysis

Multivariate statistical analysis of codon and amino acid usage

Consed: a genome sequence finishing program

Codon usage tables calculated from GenBank

DNA Assembly With Gaps: Phylogenetic aligner for sequence evolution simulation

Greedy and progressive approaches for segment-based multiple sequence alignment

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

Estimated Locations of Pattern Hits - Motif finder program

A meta-package for installing all EMBASSY packages (EMBOSS add-ons)

embassy-cbstools

EMBOSS wrappers for applications from the CBS group

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

EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications

EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA

EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs

embassy-iprscan

InterProScan motif detection add-on package for EMBOSS

embassy-memenew

EMBOSS wrappers for MEME - Multiple Em for Motif Elicitation

Fragment assembly add-on package for EMBOSS

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

EMBOSS integrated version of TOPO - Transmembrane protein display

EMBOSS integrated version of the Vienna RNA package - RNA folding

The European Molecular Biology Open Software Suite - A sequence analysis package

Additional perl modules for bioperl that can be used to easily access the EnsEMBL database

ensembl-perl-compara

Additional perl modules for bioperl that can be used to easily access the EnsEMBL database

Easy RNA Profile IdentificatioN, an RNA motif search program

Eukaryotic gene predictor

exonerate is a generic tool for pairwise sequence comparison

wxGTK monitor for the folding@home client

FASTA is a DNA and Protein sequence alignment software package

Maximum likelihood phylogenetic tree builder for DNA sequences

Fast inference of approximately-maximum-likelihood phylogenetic trees

A cross-platform graphical viewer for chromatogram files.

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

foldingathome-tools

A force field for energy calculations in proteins

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

Population genetics analysis

Generecon performs linkage disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain Monte Carlo methods.

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

An HMM-based microbial gene finding system from TIGR

An eukaryotic gene finding system from TIGR

A Genomic Mapping and Alignment Program for mRNA and EST Sequences

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).

Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

Sequence analysis using profile hidden Markov models

Inference of RNA alignments

Important Quartet Puzzling and NNI Operation

A multiple DNA sequence alignment editor

Java TreeView renders gene expression data into several interactive views.

Global and progressive multiple sequence alignment

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

Genome-scale comparison of biological sequences

Multiple sequence alignments using a variety of algorithms

MAtching Molecular Models Obtained from THeory

Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences

GUI for sci-biology/maq, a short read mapping assembler

Multiple genome alignment with large-scale evolutionary events (GUI component)

Multiple genome alignment with large-scale evolutionary events (aligner component)

Multiple alignment of large DNA sequences

The MEME/MAST system - Motif discovery and search

Statistical analysis of gene flow in pedigrees

Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina

An algorithm for finding genomic targets for microRNAs

MAtching Molecular Models Obtained from THeory

A reference-guided aligner for next-generation sequencing technologies

A suite of algorithms for ecological bioinformatics

An MPI implementation of NCBI BLAST

Bayesian Inference of Phylogeny

Identification of serial/tandem repeats in DNA sequences

A rapid whole genome aligner

Multiple sequence comparison by log-expectation

Development toolkit and applications for computational biology, including NCBI BLAST

NCBI C++ Toolkit, including NCBI BLAST+

Roche 454 pyrosequencing assembler

A phylogenetic tree drawing program which supports tree rooting

Pairwise Aligner for Long Sequences

Phylogenetic Analysis by Maximum Likelihood

GUI application written in Perl to design primers for standard PCR, bisulphite PCR and Real-time PCR

Phrap, swat, cross_match: Shotgun assembly and alignment utilities

A base caller for Sanger DNA sequencing

PHYLIP - The PHYLogeny Inference Package

Estimation of large phylogenies by maximum likelihood

Analysis of repetitive DNA found in genome sequences

Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

Whole genome association analysis toolset

Fast multiple sequence alignments using partial-order graphs

Probabilistic Alignment Kit

Design primers for PCR reactions.

A protein motif fingerprint database

Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

Multiple alignment of protein sequences with repeated and shuffled elements

A protein families and domains database

Protein Secondary Structure Prediction

Prototype ncRNA genefinder

Rapid reconstruction of phylogenies by the Neighbor-Joining method

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

Reads and writes nucleic/protein sequences in various formats.

A restriction enzyme database

A database of repetetive genetic elements in various organisms.

Screen DNA sequences for interspersed repeats and low complexity DNA

repeatmasker-libraries

A special version of RepBase used by RepeatMasker

RNA-RNA interaction search

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

roche454ace2caf

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

Pairwise protein structure alignment via double dynamic programming

A graphical multiple sequence alignment editor

A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases

SHort Read Mapping Package

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

Prediction of signal peptide cleavage sites in amino acid sequences

A program to align cDNA and genomic DNA

A library and API for manipulating large SNP datasets

The Staden Package - Biological sequence handling and analysis

A program for protein secondary structure assignment from atomic coordinates.

Calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules

A multiple sequence alignment package

The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx

A whole-genome shotgun assembler from TIGR

tigr-foundation-libs

Computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix

Prediction of transmembrane helices in proteins

A fast splice junction mapper for RNA-Seq reads

A database of eucaryotic transcription factors

Maximum likelihood analysis for nucleotide, amino acid, and two-state data.

A phylogenetic tree viewer

Tandem Repeats Finder

tRNA detection in large-scale genome sequences

TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipeline

ucsc-genome-browser

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

A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms

A sequence assembler for very short reads

The Vienna RNA Package - RNA secondary structure prediction and comparison

Whole-genome shotgun assembler based on the Celera Assembler

Intelligent algorithms for DNA searches