The FreeBSD Ports Archive
FreeBSD biology software list
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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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