The Reich laboratory studies Population Genetics & Medical Genetics.
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. It can be downloaded for LINUX (see documentation). The software package also includes the Affymetrix Human Origins Curated Dataset.
"Write to Arti Tandon if you have questions about the software and for scientific questions write to Nick Patterson." "Our program estimates the ancestry along the genome of a sample population resulting from recent admixture between two ethnic groups. The program uses data from individuals genotyped at a set of markers, where the markers chosen are preferably the ones that differ significantly in frequency between the two ancestral populations.
Ideally the user should have genotype data both for admixed samples, and for the two parental groups. The approach and algorithm have been described in detail in a paper by Patterson et al.[i] As emphasized in the paper, although controls are not required for screening of disease genes, including them can be useful, in particular for obtaining robust estimates of the marker frequencies in the ancestral populations, which is important for increasing the power of the analysis."
Method for inferring haplotype phase from genotypes for very large datasets of between 1,000 to 200,000 genotyped individuals.
"XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation can be downloaded."