PCAdmix is a software package designed to infer local ancestry along the genome of an admixed individual using genotyping data. High confidence assessment of local ancestry along the genome in admixed individuals is critical for applications such as basic ancestry inference and admixture mapping of traits for disease variants. First published as a two-way method [paper], it is now extended to three or more populations using phased data (Brisbin et al. 2012) [paper]
Download software here.
Heterozygosity EM is an Expectation-Maximization algorithm for estimating genome-wide heterozygosity from sequence data. [paper]
Download software from GitHub: [coming soon!]