Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » AIP » Software » AIP Software

AIP software

Packages  |  Licenses


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)



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