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Linux biology software

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pymol Free and Open-Source molecular modeling system
migrate A program to estimate population sizes and migration rates
clustalw CLUSTAL W Multiple Sequence Alignment Program
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

All linux biology software (ordered by name)

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
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
finchtv A chromatogram trace viewer
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
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
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