Haplotype frequency models are used to estimate the population frequency of a sequence of alleles at tightly-linked genetic loci. These models are a fundamental tool for genetic analysis because they enable analyses to use information from correlated, closely-spaced genetic variants. Haplotype frequency models are the technology underlying many important analyses, including genotype calling from low-coverage sequence data, imputation of ungenotyped markers, haplotype phasing, inference of population ancestry at a genetic locus, and detection of segments of identity-by-descent. This research will develop a more accurate and more computationally efficient haplotype frequency model, and it will develop faster, more accurate methods for haplotype phasing and genotype imputation.