biology

package name	short description	category	package developer homepage
L-Breeder-1.0	Allows you to display and breed L-system forms	biology	(Home Page)
act-2.0	A DNA sequence comparison viewer based on Artemis	biology	(Home Page)
artemis-4.0	A DNA sequence viewer and annotation tool	biology	(Home Page)
avida-1.6.0	Avida is an auto-adaptive genetic system designed for ALife research	biology	(Home Page)
babel-1.6_3	Converts among various molecular file formats	biology converters	http://smog.com/chem/babel/
biojava-1.01	Open-source java tools for processing biological data	biology java	http://www.biojava.org/
chemeq-1.10_1	Outputs LaTeX code for chemical reaction	biology textproc
clustalw-1.83	CLUSTAL W Multiple Sequence Alignment Program	biology	(Home Page)
coalesce-1.50	A program to fit population models	biology	(Home Page)
crimap-2.4	Creation of multilocus linkage maps	biology	(Home Page)
deft-2.2_2	Density functional molecular orbital calculation	biology
distribfold-0.1.20030425	distributedfolding.org distributed protein folding project	biology net	(Home Page)
dna-qc-1993.07.26	A quality control algorithm for DNA sequencing projects	biology
emboss-2.4.1_2	A collection of open source tools for genetic sequence analysis	biology	http://www.emboss.org/
fasta-20.u66	A collection of programs for searching DNA and protein databases	biology	(Home Page)
fasta3-33.t08.d4	A collection of programs for searching DNA and protein databases, v3	biology	(Home Page)
fastdnaml-1.2.2	The faster variant of DNAML, makes phylogenetic trees using maximum likelihood	biology	(Home Page)
flip-2.0.2	Flip is used to find/translate orfs	biology	(Home Page)
fluctuate-1.30	A program to fit population models	biology	(Home Page)
garlic-1.4	Molecular viewer, editor and visualization program	biology	(Home Page)
genpak-0.26_2	A set of small utilities to manipulate DNA sequences	biology	(Home Page)
gff2ps-0.97b	Converts gff-formated genomic data-sets to PostScript	biology	(Home Page)
gperiodic-2.0.6	Displays a periodic table of the elements	biology	(Home Page)
grappa-1.0.3	Genome Rearrangements Analysis and Phylogeny Software	biology	(Home Page)
hmmer-2.2.g_1	Profile hidden Markov models for biological sequence analysis	biology	http://hmmer.wustl.edu/
kinemage-5.79	A molecular visualization program with special functions	biology	(Home Page)
lamarc-2001.08.06	A package of programs for computing population parameters	biology	(Home Page)
libgenome-0.5.1	Toolkit for developing bioinformatic related software in C++	biology	http://www.libgenome.org/
lsysexp-0.67	A GTK based program for viewing and creating L-system fractals	biology	(Home Page)
migrate-1.2.4	A program to estimate population sizes and migration rates	biology	(Home Page)
molden-3.9	Display molecular orbitals and electron densities in 2D and 3D	biology	(Home Page)
mopac-7.02	Semi-empirical (MNDO, etc.) molecular orbital calculation	biology
nab-4.5.1	"This is nab (nucleic acid builder), a language for macromolecules"	biology	http://www.scripps.edu/case/
ncbi-toolkit-2003.04.21	NCBI development toolkit, including BLAST 2 and GenBank/Entrez support	biology
nclever-4.0	NClever is a character-based version of NCBI's Entrez program	biology	(Home Page)
ortep3-1.0.3_2	The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure	biology	(Home Page)
p5-AcePerl-1.83	Perl5 interface to the ACEDB genome database system	biology databases perl5	http://stein.cshl.org/AcePerl/
p5-bioperl-0.7.2	A collection of Perl modules for bioinformatics	biology perl5	http://bioperl.org/
paml-3.13	Phylogenetic Analysis by Maximum Likelihood (PAML)	biology	(Home Page)
phylip-3.6.a3	A Phylogeny Inference Package	biology	(Home Page)
platon-2001.03.09_1	Tool for viewing molecular/crystallographic structures	biology	(Home Page)
povchem-1.0_2	Simple yet powerful tool to generate POV from a PDB file	biology graphics	(Home Page)
primer3-0.9	Primer3 helps to choose primers for PCR reactions	biology	(Home Page)
psi88-1.0	Plotting wavefunctions (molecular orbitals) in 3D	biology	(Home Page)
py23-biopython-1.00.a4	A collection of Python modules for bioinformatics	biology python	http://biopython.org/
py23-martel-0.8,1	A parser generator for regular languages, written in Python	textproc biology python	(Home Page)
pymol-0.90	Free and Open-Source molecular modeling system	biology python	http://pymol.sourceforge.net/
rasmol-2.7.2_1	Fast Molecular Visualization Program	biology	(Home Page)
recombine-1.40	A program to fit population models across sites	biology	(Home Page)
ruby-bio-0.5.2	Integrated environment for Bioinformatics written in Ruby	biology ruby	(Home Page)
seaview-2003.01.21	Multiple DNA/protein sequence alignment editor	biology	(Home Page)
seqio-1.2.2	A set of C functions which can read/write biological sequence files	biology	(Home Page)
sim4-2002.03.03	An algorithm for aligning expressed DNA with genomic sequences	biology	http://globin.cse.psu.edu/
spdbv-3.7	Deep View Swiss-PdbViewer is a Protein viewer and analysis tool	biology	http://www.expasy.ch/spdbv/
tRNAscan-SE-1.21	An improved tool for transfer RNA detection	biology	(Home Page)
t_coffee-1.37	A multiple DNA or protein sequence alignment package	biology	(Home Page)
tinker-4.0	A general purpose molecular modelling package	biology	(Home Page)
treepuzzle-5.1	Maximum likelihood phylogeny reconstruction using quartets	biology	http://www.tree-puzzle.de
treeviewx-0.3	A phylogenetic tree viewer	biology	(Home Page)
wise-2.2.0	Intelligent algorithms for DNA searches	biology	(Home Page)
xdrawchem-1.7.3	Chemical drawing program	biology	(Home Page)
xmolwt-0.7	Calculate formula weight and percent of each element for a given formula	biology	(Home Page)

HOME
Events - SVBUG Events
BABE - Bay Area BSD Events
BSD Developer (Documentation, Mirrors, Benchmarks, Online Tools)
BSD Administrator (Man, Security, Ports)

About SVBUG
Past SVBUG Events
About BSD
History of BSD

Links
Site Map