Locus Technology, Inc  
   Colony management, supports creation and tracking of research animals: transgenic and congenic lines, knockouts and outbred strains.
   http://www.locustechnology.com/

The BioCatalog  
   Software directory of general interest in molecular biology and genetics.
   http://www.ebi.ac.uk/biocat/

MuStaR Sequence Variant Database Software  
   Designed to create a database of mutation loci, to make this information available to as many people as possible.
   http://www.hgu.mrc.ac.uk/Softdata/Mustar/

TagSorter  
   Database application designed to simplify the collation, sorting, comparison and identification of SAGE tag sequences.
   http://www.tagsorter.com

PopGen  
   Software that models population genetics with emphasis on genetic drift, selection, and migration.
   http://cc.oulu.fi/~jaspi/popgen/popgen.htm

Progeny Software  
   Supply pedigree drawing and genetic data management software for genetic research with a built-in customizable relational database.
   http://www.progeny2000.com

DRIFT  
   Graphically represents the effect of genetic drift on gene frequency of one or more populations for a single locus, two allele model in a closed population using stochastic simulation methods. The DOS program is free.
   http://nitro.biosci.arizona.edu/zbook/general/gened.html

Genetic Network Maps as Java Applets  
   Genetic networks controlling development in Sea Urchin represented as Java applets. Formal scheme. Molecular interactions modelled as Petri Net.
   http://www.csa.ru/Inst/gorb_dep/inbios/genet/Urchin/u0maps.htm

Hands on Genetics  
   Instructional software for basic genetics, such as DNA, PCR, Mendel, Hardy-Weinberg, meiosis and computer simulations. Download WIN and MAC demos and order online.
   http://www.handsongenetics.com

Advanced Genetics Wizard  
   Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
   http://www.geneticswizard.com

Genetics Software  
   RASA 2.2 and other Mac software for phylogenetics, comparative genomics, and sequence analysis - from Penn State University.
   http://evolution.genetics.washington.edu/phylip/software.pars.html

Istituto di Genetica Biochimica ed Evoluzionistica  
   Program that performs a permutation-based statistical test to detect genetic divergence among populations from DNA fingerprinting data . Downloadable source Fortran code, executable files and user manual .
   http://www.igbe.pv.cnr.it/software.html

Big Bench Software  
   Database application for transgenic mouse colonies. Built-in networking capabilites, for both Mac and PC. Downloadable demo version.
   http://www.bigbenchsoftware.com/

Alice Software  
   Database system to build and publish synonymised checklists of species. Species descriptions include pre-established fields and detailed descriptions employing any number of user-defined fields.
   http://www.alicesoftware.com/

STRand  
   Open-source program to automate or speed up the analysis of DNA fragment length polymorphism samples run on fluorescence based gels . Instructions for use and program download available .
   http://www.vgl.ucdavis.edu/STRand

Genetic Linkage Analysis  
   Offers links and other resources for genetic analysis software from The Rockefeller University.
   http://linkage.rockefeller.edu/

GeneticStudio  
   A complete suite of population genetic analysis programs for MAC. Includes plug-in modules.
   http://www.umsl.edu/~biology/Dyer/GeneticStudio/

PowerSSR  
   Set of statistical methods for discrete genetic data analysis, designed especially for microsatellite data analysis. Includes downloadable versions for Windows and Linux.
   http://statgen.ncsu.edu/statgen/soft_powerssr.html

The Darwin Manual  
   Guide and list of commands used to run this programming language. Library contains programs to compute pairwise alignments, phylogenetic trees, multiple sequence alignments, and to make secondary structure predictions.
   http://www.inf.ethz.ch/personal/gonnet/DarwinManual/DarwinManual.html

Statistical Genetics Software  
   Collection of primarily Fortan programs for genetic analysis. Requires registration to download.
   http://www.biomath.medsch.ucla.edu/faculty/klange/software.html

High Performance Computing and Informatics Office  
   US National Institutes of Health site with extensive genetic linkage analysis application resources on high performance computer systems. Formerly the Computational Methods and Algorithms Group.
   http://hpcio.cit.nih.gov/

CircuSoft Instrumentation LLC  
   Transgenic mouse colony tracking and management software for Mac or Windows. Includes demo software and manuals.
   http://www.circusoft.com/gmouse.html

Pegasys  
   Open source software for executing and integrating analyses of biological sequences. Includes documentation and installation instructions.
   http://www.bioinformatics.ubc.ca/pegasys/

GENtle,  
   Application for viewing and editing DNA and amino acid sequences. Integrated alignment, PCR, BLAST searches, and shared databases. Windows version is available for download (English and German).
   http://gentle.magnusmanske.de/

GeneX Virginia  
   Open source database and analysis package used to archive and analyze expression data from gene chip experiments. Includes microarray center workflow management, and researcher tools to analyze final data.
   https://genes.med.virginia.edu/

MapMakerDrawer  
   Program that draws chromosome maps (as EMF files) using the output of MapMaker EXP. Delphi source code is freely available upon request. The software is available under the MIT licence.
   http://www.emboss.co.nz/products.php?pid=2

GeneSifter.Net  
   Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation from public databases. Product overview in pdf format.
   http://www.genesifter.net/

R/qtl: A QTL Mapping Environment  
   Program for mapping quantitative trait loci in experimental crosses. Includes sample graphics and tutorial in pdf format.
   http://www.biostat.jhsph.edu/~kbroman/qtl

LAMS  
   Freeware record keeping system designed for a breeding colony of transgenic mice. Includes program description, system requirements, and installation instructions.
   http://www.hgu.mrc.ac.uk/Softdata/Lams/

Genetic Analysis Software  
   Extensive list of linkage, mapping and pedigree software with links for obtaining copies.
   http://www.nslij-genetics.org/soft/

MapPop  
   Software for selective mapping and bin mapping by Daniel Brown and Todd Vision. WIN version, documentation and references are available here.
   http://www.bio.unc.edu/faculty/vision/lab/mappop/

Broad Institute  
   GeneHunter, MapMaker, Primer, and RHMapper documentation and free software, in UNIX and C source code.
   http://www.broad.mit.edu/resources.html