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

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/

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/

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

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

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

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/

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/

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/

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

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

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

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

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

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

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/

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

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/

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

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

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/

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/

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

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

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

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

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

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

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

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

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

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