Software in animal breeding
The links on this page are still mostly dead
and outdated. Sorry for inconvenience! We have started updating them
and hopefully they will be fully functional in the near future.
If you know of an interesting software that deserves to be listed here,
please let me know (my current email address is
nvukasin@charter.net.
Educational
Estimation of variance components and prediction of genetic (BLUP) values
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ATBK - Animal Breeders
Toolkit
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ASREML estimates variance
components under a general mixed model in multivariate, spatial, repeated
measures, multi-environment and genetic analyses by REML. Detailed documentation
included.
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ASREML - A discussion group for the AsREML
software. The address of the list is asreml@chiswick.anprod.csiro.au.
To sign up, send a message to: asreml-request@chiswick.anprod.csiro.au,
with the word "subscribe" in the body of the message.
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BENDOPT and
BENDPDF: two programs implementing different approaches of the so-called
"BENDING" procedure
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DFREML
by Karin Meyer.
Estimates of (co)variance components through a derivate-free method. Programs are
provided as fortran source code for DOS and Unix. The compressed executable
is ~ 2720 Kb. Info.
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DMU
by Just Jensen. Multivariate mixed model analysis.
Versions available for IBM, Unix and PC.
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GRAMBLUP - General
Purpose Reduced Animal Model Multiple Traits BLUP Program. Download.
Some info.
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HLM - estimation
of maximum likelihood estimates of the variance-covariance components.
Commercialware.
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JAA - Mixed model
program using iteration on data with support for animal model. Download
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JSPFS - single-trait
REML program for animal models using sparse matrix solver. Download.
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MIXED procedure in
SAS. FAQs.
- Curt
Finley's comments on the usefulness of SAS PROC MIXED for animal breeders
(on the animal breeders discussion
group)
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MTCAFS (MTC)
- multitrait REML estimation of variance components program by canonical
transformation, with support for multiple random effects. Download.
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MTDFREML
(Multiple Trait Derivate Free REstricted
Maximum Likelihood)
by Curt VanTassel. Estimates of variance components and
BLUP solutions to mixed model equations.
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MTGSAM
Multiple
Trait Gibbs Sampler for Animal Models
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Quercus calculates
maximum Likelihood estimates of fixed effects and variance components.
Supplied as Pascal source code for Unix and VMS platforms. Info.
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PIGBLUP is a modern genetic
evaluation system for pigs
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VARCL
- an interactive software package for variance component analysis of hierarchically
structured data by maximum likelihood. Commercialware.
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VCE --
Multivariate multimodel REML estimation of variance components. Fortran
source code for Unix platforms. Download.
Population genetics
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GSED -
a program for the characterization of genetic structures in population
genetic investigations
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BOTTLENECK is a program for
detecting recent effective population size reductions from allele data
frequencies
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ECO-GENE
for a comprehensive evaluation of human influences on the genetic system
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FSpeed Fast Inbreeding Computation Software
- Windows program for rapidly computing the inbreeding of
all individuals in a breeding population.
Free version available.
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GDA : Software
for the Analysis of Discrete Genetic Data
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GENEPOP
computes estimates of classical population parameters. Info
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GENETIX
- a set of programs computes several basic parameters of population genetics
such as Nei's D and H, Wright's F-statistics (the Weir-Cockerham's and
Robertson-Hill's estimators), and linkage disequilibrium D
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Population and Quantitative
Genetics Software
Survival analysis
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The Survival Kit V3.0
by Vincent Ducrocq & Hans Sölkner. Cox and Weibull model, estimation of
fixed and random effects (time-dependent), estimation of hyperparameters of
the distribution of the random effects, estimation of breeding values. Suitable
for large applications.
QTL mapping & linkage analysis
Other