the phenotype but uses a multinomial model and does not account for long-range linkage disequilibrium [Lin et al., 2008]. Second, BEAGLE and PLINK can infer haplotype phase for certain forms of family data in addition to unrelated individuals. In contrast, fastPHASE, IMPUTE, MACH, and SNPMStat currently assume that all individuals are unrelated and thus ignore pedigree data that could potentially assist haplotype phasing.
