HAPI-UR is a method for inferring haplotypes in large datasets of unrelated and/or trio or duo individuals. The implementation, source code, and documentation for HAPI-UR are available here. Details of the method are in the paper Phasing of many thousands of genotyped samples.
HAPI is a method for inferring haplotypes in nuclear families that is orders of magnitude faster than other pedigree-based phasing methods. The software and documentation are available here. The algorithm is described in the paper “Rapid Haplotype Inference for Nuclear Families“. While the problem of inferring haplotypes in family data has been shown to be NP-hard, in practice HAPI has polynomial runtime. This is possible because real genotype data exhibit a relatively small number of recombinations, with few children ever showing a recombination event at the same marker position.
We developed an extension to HapMix for inferring local ancestry in multi-way admixed populations. This method was used as part of a composite method to produce local ancestry results for the 1,000 Genomes Project. Please contact Amy Williams if you are interested in using this method.
A method for simulating haplotypes resulting from pulse and/or multi-generational admixture events is available on GitHub. The method is very flexible and allows for admixture between multiple populations using arbitrary proportions of ancestry from any population in each generation.