My colleague has done some extensive work on this with a Puerto Rican population. Individuals originated from three ancestral populations: European settlers, native Taíno Indians, and West Africans. He used two programs: STRUCTURE 2.2 (Falush et al. 2003; Pritchard et al. 2000) and IAE3CI (Tsai et al. 2005; Parra et al. 2001), then the EIGENSTRAT (Price et al. 2006) program was implemented in HelixTree (Golden Helix, Bozeman, MT, USA) to calculate the principal components based on the genotypes of 100 ancestry informative markers in the population.
Added in edit 27 Jan 2012: Keep in mind that these calculations (of admixture) work best when one knows the frequencies of informative markers in each of the ancestral populations.
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