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AlphaDrop is a very simple software package for simulating genomic selection or GWAS data. It simply drops simulated haplotypes through a pedigree. The haplotypes are simulated using MaCS (Chen et al., 2009). AlphaDrop can simulate sequence and SNP data, pedigrees, QTL effects, and breeding values. Pre-specified pedigrees can also be supplied.

The user has flexibility in terms of the distribution of QTL effects required. Effects can be simulated from either normal or gamma distributions, with any number of QTL, and any restriction on the upper limit of their minor allele frequency being possible.

AlphaDrop has been used as the test framework for the development of AlphaBayes, AlphaPhase, and AlphaImpute.


For a beta test version please email John Hickey.