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Quantitative Genetics

Science > Biology > Genetics > Software > Quantitative Genetics

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

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

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

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

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

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

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

Genetic Analysis Software Database - http://www.nslij-genetics.org/soft/
Extensive, regularly-updated directory of linkage, mapping, and pedigree statistics software with links to obtain freely available copies.

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

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

http://nitro.biosci.arizona.edu/zbook/general/gened.html - http://nitro.biosci.arizona.edu/zbook/general/gened.html
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://vce.tzv.fal.de/ - http://vce.tzv.fal.de/
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-personal.une.edu.au/~bkinghor/desire.htm - http://www-personal.une.edu.au/~bkinghor/desire.htm
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/genup.htm - http://www-personal.une.edu.au/~bkinghor/genup.htm
Free software to assist learning quantitative genetic concepts (animal breeding) for WIN.

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

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

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

Laboratory of Plant Breeding, Wageningen - http://www.pbr.wur.nl/UK/Resources/
Offers free downloadable genetics and plant breeding related software.

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

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

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

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

Quantitative Genetics Resources - http://nitro.biosci.arizona.edu/zbook/book.html
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 - http://www.rqtl.org
Program for mapping quantitative trait loci in experimental crosses. Includes sample graphics and tutorial in pdf format.

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

Taxonomy 3 - http://taxonomy.delrieu.org
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 CompuPed 4.0 Pedigree Program - http://www.mbfs.com/compuped/
Extended and reverse pedigrees, inbreeding coefficients and genetic inheritance capabilities for Win and Mac. Download a demo or order online.

The Rosetta Syllego System - http://www.rosettabio.com/products/syllego/default.htm
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.

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