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 Animal Genomics and Improvement Laboratory: Beltsville, MD
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ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Genomics and Improvement Laboratory AIP Software





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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)FACTORS
A program to apply new factors for age, parity, season, and previous days open to compare cows more fairly within herds. Age-Parity-Season-PreviousDaysOpen Adjustment Factors and Software - 2023 (contact:Gary Fok)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)FIXPED
A program to check pedigree relationships and discover additional relatives (contact: Juan Nani)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.


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