Population trees represent past population divergence histories. The inference of population trees can be useful for the study of population evolution. With the size of data increases in large-scale population genetic projects, such as the 1000 Genomes Project, there are new computational challenges for ancestral population inference, including population tree inference. Existing methods for population tree inference are mainly designed for unlinked genetic variants (e.g. single nucleotide polymorphisms or SNPs). There is a potential loss of information by not considering the haplotypes.