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Haplotypes can be important to consider in association analyses. hapMC will perform haplotype associations for data from family study designs. Haplotypes are not observed directly and must be estimated from genotype data. Usually this is achieved using maximum likelihood estimates (MLE), via algorithms such as expectation-maximization (EM), but this requires that the genotype data are from independent individuals, which is not true for data in families. In hapMC, we implement a haplotype estimation method that uses a partition-ligation procedure. considers pedigree structure and considers phase uncertainly in the subsequent haplotype association test.