Bioinformatics software full list

L-Breeder: Allows you to display and breed L-system forms
act: A DNA sequence comparison viewer based on Artemis
ariadne: Programs to compare protein sequences and profiles
artemis: A DNA sequence viewer and annotation tool
avida: Avida is an auto-adaptive genetic system designed for ALife research
babel: Converts among various molecular file formats
biojava: Open-source java tools for processing biological data
bioperl: openfree Biological perl module.
chemeq: Outputs LaTeX code for chemical reaction
clustalw: CLUSTAL W Multiple Sequence Alignment Program
mrbayes: Bayesian inference of phylogeny
coalesce: A program to fit population models
crimap: Creation of multilocus linkage maps
deft: Density functional molecular orbital calculation
distribfold: distributedfolding.org distributed protein folding project
dna-qc: A quality control algorithm for DNA sequencing projects
emboss: A collection of open source tools for genetic sequence analysis
fasta: A collection of programs for searching DNA and protein databases
fasta3: A collection of programs for searching DNA and protein databases
fastdnaml: Faster DNAML, makes phylogenetic trees using maximum likelihood
flip: Flip is used to find/translate orfs
fluctuate: A program to fit population models
garlic: Molecular viewer, editor and visualization program
genpak: A set of small utilities to manipulate DNA sequences
gff2ps: Converts gff-formated genomic data-sets to PostScript
gperiodic: Displays a periodic table of the elements
grappa: Genome Rearrangements Analysis and Phylogeny Software
hmmer: Profile hidden Markov models for biological sequence analysis
kinemage: A molecular visualization program with special functions
lamarc: A package of programs for computing population parameters
Linguamatics: High performance text mining software to analyze scientific literature, patents & other sources
linux-foldingathome: Distributed client for Protein Folding
libgenome: Toolkit for developing bioinformatic related software in C++
lsysexp: A GTK based program for viewing and creating L-system fractals
migrate: A program to estimate population sizes and migration rates
molden: Display molecular orbitals and electron densities in 2D and 3D
mopac: Semi-empirical (MNDO, etc.) molecular orbital calculation
nab: A language for macromolecules
ncbi-toolkit: NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
nclever: NClever is a character-based version of NCBI's Entrez program
ortep3: The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
p5-AcePerl: Perl5 interface to the ACEDB genome database system
p5-bioperl: A collection of Perl modules for bioinformatics
paml: Phylogenetic Analysis by Maximum Likelihood (PAML)
phylip: A Phylogeny Inference Package
platon: Tool for viewing molecular/crystallographic structures
povchem: Simple yet powerful tool to generate POV from a PDB file
primer3: Primer3 helps to choose primers for PCR reactions
psi88: Plotting wavefunctions (molecular orbitals) in 3D
py-biopython: A collection of Python modules for bioinformatics
pymol: Free and Open-Source molecular modeling system
rasmol: Fast Molecular Visualization Program
recombine: A program to fit population models across sites
ruby-bio: Integrated environment for Bioinformatics written in Ruby
seaview: Multiple DNA/protein sequence alignment editor
seqio: A set of C functions which can read/write biological sequence files
sim4: An algorithm for aligning expressed DNA with genomic sequences
spdbv: Deep View Swiss-PdbViewer is a Protein viewer and analysis tool
tRNAscan-SE: An improved tool for transfer RNA detection
t_coffee: A multiple DNA or protein sequence alignment package
tinker: A general purpose molecular modelling package
treepuzzle: Maximum likelihood phylogeny reconstruction using quartets
treeviewx: A phylogenetic tree viewer
wise: Intelligent algorithms for DNA searches
xdrawchem: Chemical drawing program
xmolwt: Calculate formula weight and percent of each element for a given formula
blast: WU BLAST, a software package for sequence similarity searches
embassy: A collection of contributed EMBOSS applications
p5-Bio-ASN1-EntrezGene: Regular expression-based Perl Parser for NCBI Entrez Gene
p5-Bio-Das: Client-side library for Distributed Genome Annotation System
adun: Molecular Simulator for GNUstep
belvu: A viewer for multiple sequence alignments
biococoa: Bioinformatics framework
blat: A fast tool for local sequence similarity searches
boinc-simap: Similarity Matrix of Proteins project for BOINC
dotter: A viewer for multiple sequence alignments
gmap: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
jalview: A viewer and editor for multiple sequence alignments
lagan: Efficient tools for large-scale multiple alignments of genomic DNA
mafft: Multiple sequence alignments based on fast Fourier transform
p5-Bio-Phylo: Phylogenetic analysis using perl
p5-bioperl-devel: A collection of Perl modules for bioinformatics (developer release)
p5-bioperl-run: Wrapper modules for common bioinformatics tools
p5-bioperl-run-devel: Wrapper modules for common bioinformatics tools (developer release)
protomol: OO, component based, framework for molecular dynamics (MD) simulations
mummer: A modular system for rapid whole genome alignment