The issue of haplotype estimation (phasing) is by now quite well-studied in human genetics. Estimated haplotypes are routinely used for a variety of downstream analyses, including estimation of recombination rates,28 measurement of linkage disequilibrium,29 and genotype imputation.30 This desire to construct (potentially long-range) haplotypes, given unphased genotype data, has resulted in the development of a variety of software packages that can efficiently perform haplotype estimation on a chromosome-wide scale. Arguably one of the most competitive among these is the package SHAPEIT2,31,32 which has been found to outperform most other methods in terms of switch error rate and high computational efficiency.32 Although designed primarily for the analysis of unrelated individuals, SHAPEIT2 also has the advantage of being able to handle case-parent trios and duos. (These situations impose constraints on the configurations of possible haplotypes that are consistent within a duo or trio.) Given the availability of such a convenient software implementation for haploype phasing (in the form of SHAPEIT2), we sought to update our software suite, PREMIM and EMIM, to make use of haplotypes estimated with SHAPEIT2, in order to provide improved power for detection of parent-of-origin effects. Here, we present an overview and evaluation of our improved method, which has been incorporated into our freely available software package PREMIM and EMIM.21