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Amino acid indices and similarity matrices

ABI-connectivity-data

ABI-expression-data

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

Eukaryotic gene predictor

Blat-like Fast Accurate Search Tool

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

A generic bioinformatics relational database model

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

An ultrafast memory-efficient short read aligner

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

cd-hit-auxtools

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

Consed: a genome sequence finishing program

Codon usage tables calculated from GenBank

dargcc_bidsdata

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

drlfom_bidsdata

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-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

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

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

Eukaryotic gene predictor

exonerate is a generic tool for pairwise sequence comparison

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

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

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

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

irsabi_bidsdata

KaKs_Calculator

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

lemur-brain-atlas

Multiple sequence alignments using a variety of algorithms

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

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

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

A reference-guided aligner for next-generation sequencing technologies

A suite of algorithms for ecological bioinformatics

mouse-brain-atlases

Bayesian Inference of Phylogeny

A rapid whole genome aligner

Multiple sequence comparison by log-expectation

ncbi-genome-download

Development toolkit and applications for computational biology, including NCBI BLAST

NGSEPplugin-bin

A phylogenetic tree drawing program which supports tree rooting

opfvta_bidsdata

Pairwise Aligner for Long Sequences

Phylogenetic Analysis by Maximum Likelihood

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

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

A protein families and domains database

Protein Secondary Structure Prediction

Prototype ncRNA genefinder

rat-brain-atlases

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

A restriction enzyme database

Screen DNA sequences for interspersed repeats and low complexity DNA

repeatmasker-libraries

A special version of RepBase used by RepeatMasker

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

roche454ace2caf

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

Scaffolder-evaluation

scaffold_builder

scan_for_matches

A graphical multiple sequence alignment editor

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

A program to align cDNA and genomic DNA

A program for protein secondary structure assignment from atomic coordinates.

A multiple sequence alignment package

tigr-foundation-libs

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

ucsc-genome-browser

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

A sequence assembler for very short reads

VelvetOptimiser

Whole-genome shotgun assembler based on the Celera Assembler

Intelligent algorithms for DNA searches