bag8ger, loathe as I am to discuss the LSHTM's ADMIXMAP PROGRAM (given the propensity of certain idiots to try to confuse people), the simple answer is that allele frequencies in the subpopulations under investigation is one of the inputs provided by the user of the program. The program itself is available via the web for anyone to download and use, although the LSHTM suggest that prospective users contact them first to discuss their requirements.