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