SNPEM is used to assess the accuracy of haplotype frequency estimation as a function of such factors as sample size, number of loci studied, allele frequencies and locus-specific allelic departures from Hardy-Weinberg and linkage equilibrium. Many haplotype-analysis methods require phase information, which can be difficult to obtain from samples of non-haploid species. SNPEM, which employs strategies for estimating haplotype frequencies from unphased diploid genotype data collected on a sample of individuals, uses the expectation-maximization (EM) algorithm to overcome the missing phase information. SNPEM, which was developed by Nicholas J. Schork, Ph.D., Director of Biostatistics and Bioinformatics at STSI, is protected by U.S. patent.
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