the entire directory only in Software/Quantitative_Genetics

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• Genetic Analysis Software Database - Extensive, regularly-updated directory of linkage, mapping, and pedigree statistics software with links to obtain freely available copies.
• 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.
• Agriculture Business Research Institute - ABRI provides recording systems for all species of commercial livestock. Software offered include Dairy Express, Saltbush and Breedplan.
• Big Bench Software - Commercial software for the management of transgenic mouse colonies. Windows and Mac OS X. Demo version available.
• DESIRE - Explore possible selection outcomes when goals (desired gains) are set for traits. This free WIN program is also contained in GENUP.
• 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.
• Finnish Forest Genetics and Tree Breeding - Links to population and quantitative genetic software of interest in tree improvement, but also useful in other species.
• 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.
• Genup - Free software to assist learning quantitative genetic concepts (animal breeding) for WIN.
• Ignacy Misztal - Animal breeding oriented programs for sparse matrix multiple trait REML and BLUP. Fortran source is free for research use.
• LAMS - Freeware record keeping system designed for a breeding colony of transgenic mice. Includes program description, system requirements, and installation instructions.
• Laboratory of Plant Breeding, Wageningen - Offers free downloadable genetics and plant breeding related software.
• Locus Technology, Inc - Colony management, supports creation and tracking of research animals and for transgenic and congenic lines, knockouts and outbred strains.
• MapPop - Software for selective mapping and bin mapping. Windows version, documentation and references are available for download.
• Mosaic Vivarium - Web-based software tool for breeding colony management. The software is well-suited to management of transgenic and genetically-modified mouse breeding colonies.
• Pedigree Viewer - Unique display and examination tool for large pedigrees, with inbreeding and genetic merit data also. Free WIN program.
• PopGen - Software that models population genetics with emphasis on genetic drift, selection, and migration. Windows 95.
• PowerMarker - Set of statistical methods for discrete genetic data analysis, designed especially for microsatellite data analysis. Includes downloadable versions for Windows.
• Progeny Software - Supply pedigree drawing and genetic data management software for genetic research with a built-in customizable relational database.
• 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.
• R/qtl: A QTL Mapping Environment - Program for mapping quantitative trait loci in experimental crosses. Includes sample graphics and tutorial in pdf format.
• Statistical Genetics Software - Collection of primarily Fortan 77 programs for genetic analysis. Requires registration to download. Site not updated since 1999.
• 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.
• 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.
• 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.

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