aaindex

Amino acid indices and similarity matrices

amap

Protein multiple-alignment-based sequence annealing

ariadne

Protein sequences and profiles comparison

bioperl

Perl tools for bioinformatics - Core modules

bioperl-run

Perl tools for bioinformatics - Analysis run modules

biopython

Biopython - Python modules for computational molecular biology

bioruby

An integrated environment for bioinformatics using the Ruby language

clustalw

General purpose multiple alignment program for DNA and proteins

clustalw-mpi

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

clustalx

Graphical interface for the ClustalW multiple alignment program

cutg

Codon usage tables calculated from GenBank

dialign-t

An improved algorithm for segment-based multiple sequence alignment

elph

Estimated Locations of Pattern Hits - Motif finder program

embassy

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

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

embassy-emnu

EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications

embassy-esim4

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

embassy-hmmer

EMBOSS integrated version of HMMER - Biological sequence analysis with profile HMMs

embassy-meme

EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation

embassy-memenew

EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation

embassy-mse

EMBOSS integrated version of MSE - Multiple Sequence Screen Editor

embassy-phylip

EMBOSS integrated version of the PHYLogeny Inference Package

embassy-phylipnew

EMBOSS integrated version of the PHYLogeny Inference Package

embassy-signature

Protein signature add-on package for EMBOSS

embassy-structure

Protein structure add-on package for EMBOSS

embassy-topo

EMBOSS integrated version of TOPO - Transmembrane protein display

embassy-vienna

RNA folding add-on package for EMBOSS

emboss

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

finchtv

A cross-platform graphical viewer for chromatogram files.

foldingathome

Help simulate protein folding at home

gibbs

A Gibbs sampling algorithm for local alignment of subtle sequence signals in multiple protein sequences.

hmmer

Sequence analysis using profile hidden Markov models

mafft

Multiple sequence alignments using a variety of algorithms

mammoth

MAtching Molecular Models Obtained from THeory

meme

The MEME/MAST system - Motif discovery and search

mrbayes

Bayesian Inference of Phylogeny

muscle

Multiple sequence comparison by log-expectation

ncbi-tools

Development toolkit and applications for computational biology

njplot

A phylogenetic tree drawing program which supports tree rooting

paml

Phylogenetic Analysis by Maximum Likelihood

phylip

PHYLIP - The PHYLogeny Inference Package

phyml

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

poa

Fast multiple sequence alignments using partial-order graphs

primer3

Design primers for PCR reactions.

prints

A protein motif fingerprint database

probcons

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

prosite

A protein families and domains database

qrna

Prototype ncRNA genefinder

readseq

Reads and writes nucleic/protein sequences in various formats.

rebase

A restriction enzyme database

rnaview

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

seaview

A graphical multiple sequence alignment editor

sim4

A program to align cDNA and genomic DNA

staden-bin

The Staden Package - Biological sequence handling and analysis

stride

A program for protein secondary structure assignment from atomic coordinates.

t-coffee

A multiple sequence alignment package

transfac

A database of eucaryotic transcription factors

tree-puzzle

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

treeviewx

A phylogenetic tree viewer

trnascan-se

tRNA detection in large-scale genome sequences

vienna-rna

Vienna RNA Package - RNA secondary structure prediction and comparison

wise

Intelligent algorithms for DNA searches

aaindex

embassy-mse

phyml

amap

embassy-phylip

poa

ariadne

embassy-phylipnew

primer3

bioperl

embassy-signature

prints

bioperl-run

embassy-structure

probcons

biopython

embassy-topo

prosite

bioruby

embassy-vienna

qrna

clustalw

emboss

readseq

clustalw-mpi

finchtv

rebase

clustalx

foldingathome

rnaview

cutg

gibbs

seaview

dialign-t

hmmer

sim4

elph

mafft

staden-bin

embassy

mammoth

stride

embassy-domainatrix

meme

t-coffee

embassy-domalign

mrbayes

transfac

embassy-domsearch

muscle

tree-puzzle

embassy-emnu

ncbi-tools

treeviewx

embassy-esim4

njplot

trnascan-se

embassy-hmmer

paml

vienna-rna

embassy-meme

phylip

wise

embassy-memenew