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United States Department of Agriculture

Agricultural Research Service

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ANIMAL IMPROVEMENT
PROGRAM

AIP Software

AIP software


Packages  |  Licenses

Packages

  • BESTPRED – A set of programs for best prediction of lactation yields (contact: John Cole)

  • ConvertCufflinksToExcel – A program to convert Cufflinks output files into easily readable Microsoft Excel tables using Apache's POI library (only "cuffdiff" output format currently supported; contact: Derek Bickhart)

  • FINDHAP – A program to find haplotypes and impute genotypes from multiple marker sets and sequence data (contact: Paul VanRaden)

  • FINDMAP – A program to align sequence reads to reference map, call previous variants, and identify new variants (contact: Paul VanRaden)

  • GENOSIM – A set of programs to simulate genotypes, breeding values, phenotypes, and DNA sequence read depth and to resolve SNP conflicts between parent and offspring genotypes (contact: Paul VanRaden)

  • MTDFREML – A set of programs for estimation of genetic (co)variances using multiple-trait derivative-free restricted maximum likelihood (contact: Curt Van Tassell)

  • MTGSAM – A multiple-trait Gibbs sampler for animal models (contact: Curt Van Tassell)


    • Licenses

    All AIP software is in the public domain and may be modified and redistributed at will.


    Last Modified:


    Last Modified: 01/12/2017