Quantitative Genetics

Agriculture Business Research Institute
ABRI provides recording systems for all species of commercial livestock. Software offered include Dairy Express, Saltbush and Breedplan.
http://abri.une.edu.au

Animal Breeding & Genetics, Wageningen
Provides programmes in the area of animal breeding including SIP (Selection Index Program), MAGGIC (Gibbs Sampling) and GENEFLOW. Free software for WIN.
http://www.zod.wau.nl/abg/hs/links/software.html

ASReml Cookbook
Statistical software designed for fitting mixed models for large datasets. Contains commented code for univariate and multivariate analysis including longitudinal and spatial analysis.
http://uncronopio.org/ASReml

Big Bench Software
Commercial software for the management of transgenic mouse colonies. Windows and Mac OS X. Demo version available.
http://www.bigbenchsoftware.com/

CircuSoft Instrumentation LLC
Transgenic mouse colony tracking and management software for the Mac and Windows. Includes demo software and manuals.
http://www.circusoft.com/content/product/1/

The CompuPed 4.0 Pedigree Program
Extended and reverse pedigrees, inbreeding coefficients and genetic inheritance capabilities for Win and Mac. Download a demo or order online.
http://www.mbfs.com/compuped/

DESIRE
Explore possible selection outcomes when goals (desired gains) are set for traits. This free WIN program is also contained in GENUP.
http://www-personal.une.edu.au/~bkinghor/desire.htm

DFREML
Meyer's variance component estimation software for animal breeding is free for research purposes, available for UNIX, DOS and FORTRAN source code.
http://agbu.une.edu.au/~kmeyer/dfreml.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

Finnish Forest Genetics and Tree Breeding
Links to population and quantitative genetic software of interest in tree improvement, but also useful in other species.
http://www.metla.fi/info/vlib/forestgen/software.htm

GeneFlow Inc
This Virginia, USA company provides software (GeneFlow, SynerGene, QTLlocate) and services oriented towards plant breeding. Website does not give prices or operating systems supported.
http://www.geneflowinc.com/

GeneticStudio
Software platform targeting the analysis of population genetic data. Provides some brief videos to demonstrate the application.
http://dyerlab.bio.vcu.edu/trac/GeneticStudio

Genup
Free software to assist learning quantitative genetic concepts (animal breeding) for WIN.
http://www-personal.une.edu.au/~bkinghor/genup.htm

Ignacy Misztal
Animal breeding oriented programs for sparse matrix multiple trait REML and BLUP. Fortran source is free for research use.
http://nce.ads.uga.edu/~ignacy/programs.html

Laboratory of Plant Breeding, Wageningen
Offers free downloadable genetics and plant breeding related software.
http://www.dpw.wau.nl/pv/

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 and for transgenic and congenic lines, knockouts and outbred strains.
http://www.locustechnology.com/

MapPop
Software for selective mapping and bin mapping. Windows version, documentation and references are available for download.
http://www.bio.unc.edu/faculty/vision/lab/mappop/

Mosaic Vivarium
Web-based software solution for breeding colony management. The software is well-suited to management of transgenic and genetically-modified mouse breeding colonies.
http://www.mosaicvivarium.com

Pedigree Viewer
Unique display and examination tool for large pedigrees, with inbreeding and genetic merit data also. Free WIN program.
http://www-personal.une.edu.au/~bkinghor/pedigree.htm

PopGen
Software that models population genetics with emphasis on genetic drift, selection, and migration. Windows 95.
http://cc.oulu.fi/~jaspi/popgen/popgen.htm

PowerMarker
Set of statistical methods for discrete genetic data analysis, designed especially for microsatellite data analysis. Includes downloadable versions for Windows.
http://statgen.ncsu.edu/powermarker/

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

Quantitative Genetics Resources
List of resources with links to programs and notes on a range of subjects including animal and plant breeding, and evolutionary and human genetics.
http://nitro.biosci.arizona.edu/zbook/book.html

The Rosetta Syllego System
The system is a resource for managing genetic variation information and integrating relevant study data from various sources so that scientists and researchers can better plan and execute genetic studies.
http://www.rosettabio.com/products/syllego/default.htm

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.rqtl.org

Statistical Genetics Software
Collection of primarily Fortan 77 programs for genetic analysis. Requires registration to download. Site not updated since 1999.
http://www.biomath.medsch.ucla.edu/faculty/klange/software.html

Taxonomy 3
A package of SAS macros for target discovery, detection of subphenotype and genetic heterogeneity. Can use an unlimited numbers of markers in a single multivariate analysis.
http://taxonomy.delrieu.org

VCE
Groeneveld's Variance Component Estimation software was developed for animal breeding problems. WIN and UNIX versions are free for research use. PEST documentation is also available here.
http://www.tzv.fal.de/~eg/