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Software related to biology.

L-Breeder-1.0
Allows you to display and breed L-system forms
Long description | Sources | Main Web Site
Maintained by: dyeske@yahoo.com
Requires: Mesa-3.4.2_2, XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gdk-pixbuf-0.22.0, gettext-0.11.5_1, glib-1.2.10_9, gmake-3.80, gtk-1.2.10_9, imake-4.3.0_1, jpeg-6b_1, libiconv-1.9.1_1, pkgconfig-0.15.0, png-1.2.5_2, tiff-3.5.7_1, wxgtk-2.2.9,1
act-2.0
A DNA sequence comparison viewer based on Artemis
Long description | Sources | Main Web Site
Maintained by: chuynh@biolateral.com.au
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gettext-0.11.5_1, glib-1.2.10_9, gtk-1.2.10_9, imake-4.3.0_1, javavmwrapper-1.4, jdk-1.3.1p8_2, libiconv-1.9.1_1, nspr-4.3_2, open-motif-2.2.2_1, pkgconfig-0.15.0, urwfonts-1.0
artemis-4.0
A DNA sequence viewer and annotation tool
Long description | Sources | Main Web Site
Maintained by: chuynh@biolateral.com.au
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gettext-0.11.5_1, glib-1.2.10_9, gtk-1.2.10_9, imake-4.3.0_1, javavmwrapper-1.4, jdk-1.3.1p8_2, libiconv-1.9.1_1, nspr-4.3_2, open-motif-2.2.2_1, pkgconfig-0.15.0, urwfonts-1.0
avida-1.6.0
Avida is an auto-adaptive genetic system designed for ALife research
Long description | Sources | Main Web Site
Maintained by: karlj000@unbc.ca
Requires: expat-1.95.6_1, gettext-0.11.5_1, gmake-3.80, libiconv-1.9.1_1
babel-1.6_3
Converts among various molecular file formats
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Also listed in: Converters
biojava-1.01
Open-source java tools for processing biological data
Long description | Sources | Main Web Site
Maintained by: bio@freebsd.net
Requires: javavmwrapper-1.4, linux-sun-jdk-1.2.2.015, linux_base-7.1_5
Also listed in: Java
chemeq-1.10_1
Outputs LaTeX code for chemical reaction
Long description | Sources
Maintained by: rmiya@cc.hirosaki-u.ac.jp
Requires: bison-1.75, expat-1.95.6_1, gettext-0.11.5_1, libiconv-1.9.1_1, m4-1.4_1
Also listed in: Textproc
clustalw-1.83
CLUSTAL W Multiple Sequence Alignment Program
Long description | Sources | Main Web Site
Maintained by: dbader@eece.unm.edu
coalesce-1.50
A program to fit population models
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
crimap-2.4
Creation of multilocus linkage maps
Long description | Sources | Main Web Site
Maintained by: tonym@biolateral.com.au
deft-2.2_2
Density functional molecular orbital calculation
Long description | Sources
Maintained by: rmiya@cc.hirosaki-u.ac.jp
Requires: f2c-3.0.0, f77-0.3, fpp-1.1
distribfold-0.1.20030425
distributedfolding.org distributed protein folding project
Long description | Sources | Main Web Site
Maintained by: lioux@FreeBSD.org
Also listed in: Net
dna-qc-1993.07.26
A quality control algorithm for DNA sequencing projects
Long description | Sources
Maintained by: tonym@biolateral.com.au
emboss-2.4.1_1
A collection of open source tools for genetic sequence analysis
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gd-2.0.15, gettext-0.11.5_1, gmake-3.80, imake-4.3.0_1, jpeg-6b_1, libiconv-1.9.1_1, open-motif-2.2.2_1, pkgconfig-0.15.0, png-1.2.5_2
fasta-20.u66
A collection of programs for searching DNA and protein databases
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
fasta3-33.t08.d4
A collection of programs for searching DNA and protein databases, v3
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
fastdnaml-1.2.2
The faster variant of DNAML, makes phylogenetic trees using maximum likelihood
Long description | Sources | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: expat-1.95.6_1, gettext-0.11.5_1, gmake-3.80, libiconv-1.9.1_1
flip-2.0.2
Flip is used to find/translate orfs
Long description | Sources | Main Web Site
Maintained by: tonym@biolateral.com.au
fluctuate-1.30
A program to fit population models
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
genpak-0.26_1
GP is a set of small utilities to manipulate DNA sequences
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gd-2.0.15, gettext-0.11.5_1, gmake-3.80, imake-4.3.0_1, jpeg-6b_1, libiconv-1.9.1_1, pkgconfig-0.15.0, png-1.2.5_2
gff2ps-0.97b
Converts gff-formated genomic data-sets to PostScript
Long description | Sources | Main Web Site
Maintained by: chuynh@biolateral.com.au
Requires: bash-2.05b.007, gawk-3.1.1
gperiodic-1.3.3
Displays a periodic table of the elements
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gettext-0.11.5_1, glib-1.2.10_9, gmake-3.80, gtk-1.2.10_9, imake-4.3.0_1, libiconv-1.9.1_1, pkgconfig-0.15.0
grappa-1.0.3
Genome Rearrangements Analysis and Phylogeny Software
Long description | Sources | Main Web Site
Maintained by: dbader@eece.unm.edu
Requires: concorde-1.0_1, expat-1.95.6_1, gettext-0.11.5_1, gmake-3.80, libiconv-1.9.1_1
hmmer-2.2.g_1
Profile hidden Markov models for biological sequence analysis
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
kinemage-5.79
A molecular visualization program with special functions
Long description | Sources | Main Web Site
Maintained by: jeremy@external.org
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, open-motif-2.2.2_1, pkgconfig-0.15.0
lamarc-2001.08.06
A package of programs for computing population parameters
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
Requires: coalesce-1.50, fluctuate-1.30, migrate-1.2.4, recombine-1.40
libgenome-0.5.1
Toolkit for developing bioinformatic related software in C++
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: libtool-1.3.5_1
migrate-1.2.4
A program to estimate population sizes and migration rates
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
molden-3.9
Display molecular orbitals and electron densities in 2D and 3D
Long description | Sources | Main Web Site
Maintained by: rmiya@cc.hirosaki-u.ac.jp
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, pkgconfig-0.15.0
mopac-7.02
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Sources
Maintained by: rmiya@cc.hirosaki-u.ac.jp
Requires: expat-1.95.6_1, f2c-3.0.0, f77-0.3, fpp-1.1, gettext-0.11.5_1, gmake-3.80, libiconv-1.9.1_1
nab-4.5.1
"This is nab (nucleic acid builder), a language for macromolecules"
Long description | Sources | Main Web Site
Maintained by: bdodson@scms.utmb.edu
Requires: ucpp-1.2_1
ncbi-toolkit-2003.04.21
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Sources
Maintained by: tonym@biolateral.com.au
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, open-motif-2.2.2_1, pkgconfig-0.15.0
nclever-4.0
NClever is a character-based version of NCBI's Entrez program
Long description | Sources | Main Web Site
Maintained by: tonym@biolateral.com.au
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, ncbi-toolkit-2003.04.21, open-motif-2.2.2_1, pkgconfig-0.15.0
ortep3-1.0.3_2
The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
Long description | Sources | Main Web Site
Maintained by: rmiya@cc.hirosaki-u.ac.jp
p5-AcePerl-1.83
Perl5 interface to the ACEDB genome database system
Long description | Sources | Main Web Site
Maintained by: philip@p6m7g8.com
Requires: p5-Digest-MD5-2.24
Also listed in: Databases, Perl5
p5-bioperl-0.7.2
A collection of Perl modules for bioinformatics
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
Requires: expat-1.95.6_1, p5-AcePerl-1.83, p5-Authen-SASL-2.04, p5-Digest-MD5-2.24, p5-File-Spec-0.82, p5-File-Temp-0.12_1, p5-HTML-Parser-3.28, p5-HTML-Tagset-3.03, p5-IO-String-1.02, p5-IO-stringy-2.108, p5-MIME-Base64-2.20, p5-Net-1.12,1, p5-URI-1.23, p5-XML-Node-0.10, p5-XML-Parser-2.31_1, p5-XML-Writer-0.4_1, p5-libwww-5.69, p5-libxml-0.07
Also listed in: Perl5
p5-bioperl-devel-0.9.0
A collection of Perl modules for bioinformatics (developer's release)
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
Requires: expat-1.95.6_1, libiconv-1.9.1_1, p5-AcePerl-1.83, p5-Authen-SASL-2.04, p5-Digest-MD5-2.24, p5-File-Spec-0.82, p5-File-Temp-0.12_1, p5-HTML-Parser-3.28, p5-HTML-Tagset-3.03, p5-IO-String-1.02, p5-IO-stringy-2.108, p5-MIME-Base64-2.20, p5-Net-1.12,1, p5-Text-Iconv-1.2_1, p5-URI-1.23, p5-XML-Node-0.10, p5-XML-Parser-2.31_1, p5-XML-Twig-3.09, p5-XML-Writer-0.4_1, p5-libwww-5.69, p5-libxml-0.07
Also listed in: Perl5
paml-3.13
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Sources | Main Web Site
Maintained by: dbader@eece.unm.edu
phylip-3.6.a3
A Phylogeny Inference Package
Long description | Sources | Main Web Site
Maintained by: dbader@eece.unm.edu
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, pkgconfig-0.15.0
platon-2001.03.09_1
Tool for viewing molecular/crystallographic structures
Long description | Sources | Main Web Site
Maintained by: rmiya@cc.hirosaki-u.ac.jp
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, pkgconfig-0.15.0
povchem-1.0_2
Simple yet powerful tool to generate POV from a PDB file
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, jpeg-6b_1, pkgconfig-0.15.0, png-1.2.5_2, povray-3.5_2, svgalib-1.4.2_1, tiff-3.5.7_1
Also listed in: Graphics
primer3-0.9
Primer3 helps to choose primers for PCR reactions
Long description | Sources | Main Web Site
Maintained by: tonym@biolateral.com.au
psi88-1.0
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Sources | Main Web Site
Maintained by: rmiya@cc.hirosaki-u.ac.jp
py22-biopython-1.00.a4
A collection of Python modules for bioinformatics
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
Requires: py22-martel-0.8,1, py22-mx-base-2.0.4, py22-numeric-21.0, py22-reportlab-1.17, python-2.2.3_2
Also listed in: Python
py22-martel-0.8,1
A parser generator for regular languages, written in Python
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
Requires: py22-mx-base-2.0.4, python-2.2.3_2
Also listed in: Textproc, Python
pymol-0.90
Free and Open-Source molecular modeling system
Long description | Sources | Main Web Site
Maintained by: maho@FreeBSD.org
Requires: Mesa-3.4.2_2, XFree86-libraries-4.3.0_5, blt-2.4u, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gettext-0.11.5_1, gmake-3.80, imake-4.3.0_1, libiconv-1.9.1_1, pkgconfig-0.15.0, png-1.2.5_2, py22-numeric-21.0, py22-pmw-1.1, py22-tkinter-2.2.3, python-2.2.3_2, tcl-8.3.5_2, tk-8.3.5_2
Also listed in: Python
rasmol-2.7.2_1
Fast Molecular Visualization Program
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, pkgconfig-0.15.0
recombine-1.40
A program to fit population models across sites
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
ruby-bio-0.5.0
Integrated environment for Bioinformatics written in Ruby
Long description | Sources | Main Web Site
Maintained by: knu@FreeBSD.org
Requires: ruby-1.8.0.p3.2003.06.25_1
Also listed in: Ruby
seaview-2003.01.21
Multiple DNA/protein sequence alignment editor
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: Mesa-3.4.2_2, XFree86-libraries-4.3.0_5, expat-1.95.6_1, fltk-1.1.3, fontconfig-2.2.90_3, freetype2-2.1.4_1, imake-4.3.0_1, jpeg-6b_1, pkgconfig-0.15.0, png-1.2.5_2
seqio-1.2.2
A set of C functions which can read/write biological sequence files
Long description | Sources | Main Web Site
Maintained by: tonym@biolateral.com.au
sim4-2002.03.03
An algorithm for aligning expressed DNA with genomic sequences
Long description | Sources | Main Web Site
Maintained by: bio@freebsd.net
spdbv-3.7
Deep View Swiss-PdbViewer is a Protein viewer and analysis tool
Long description | Sources | Main Web Site
Maintained by: chuynh@biolateral.com.au
Requires: linux-openmotif-2.1.30, linux_base-7.1_5, linux_mesa-3.4.2_1
tRNAscan-SE-1.21
An improved tool for transfer RNA detection
Long description | Sources | Main Web Site
Maintained by: chuynh@biolateral.com.au
t_coffee-1.37
A multiple DNA or protein sequence alignment package
Long description | Sources | Main Web Site
Maintained by: wjv@FreeBSD.org
Requires: clustalw-1.83
tinker-4.0
A general purpose molecular modelling package
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
treepuzzle-5.1
Maximum likelihood phylogeny reconstruction using quartets
Long description | Sources | Main Web Site
Maintained by: jan.lentfer@web.de
treeviewx-0.3
A phylogenetic tree viewer
Long description | Sources | Main Web Site
Maintained by: tonym@biolateral.com.au
Requires: Mesa-3.4.2_2, XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gettext-0.11.5_1, glib-1.2.10_9, gmake-3.80, gtk-1.2.10_9, imake-4.3.0_1, jpeg-6b_1, libiconv-1.9.1_1, pkgconfig-0.15.0, png-1.2.5_2, tiff-3.5.7_1, wxgtk-2.4.0
wise-2.2.0
Intelligent algorithms for DNA searches
Long description | Sources | Main Web Site
Maintained by: tonym@biolateral.com.au
xdrawchem-0.99.7
Chemical drawing program
Long description | Sources | Main Web Site
Maintained by: trevor@FreeBSD.org
Requires: Mesa-3.4.2_2, XFree86-libraries-4.3.0_5, Xft-2.1.2, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gettext-0.11.5_1, gmake-3.80, imake-4.3.0_1, jpeg-6b_1, lcms-1.09,1, libiconv-1.9.1_1, libmng-1.0.5, pkgconfig-0.15.0, png-1.2.5_2, qt-2.3.1_2
xmolwt-0.7
Calculate formula weight and percent of each element for a given formula
Long description | Sources | Main Web Site
Maintained by: rmiya@cc.hirosaki-u.ac.jp
Requires: XFree86-libraries-4.3.0_5, expat-1.95.6_1, fontconfig-2.2.90_3, freetype2-2.1.4_1, gettext-0.11.5_1, glib-1.2.10_9, gmake-3.80, gtk-1.2.10_9, imake-4.3.0_1, libiconv-1.9.1_1, pkgconfig-0.15.0
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Last modified: 13-August-2003