MALDSoft is a program for admixture mapping, a promising new tool for discovering genes that contribute to complex traits. This mapping approach uses samples from recently admixed populations to detect susceptibility loci at which the risk alleles have different frequencies in the original contributing populations. The program can use genotype data from cases only and both cases and controls. Additional 'learning' samples representative of the contributing populations can also be used. Ancestral states along chromosomes are modelled as hidden Markov chains. The figure shows an example of real versus estimated ancestry by using two different map densities. See Montana and Pritchard (2004) for methodological details and simulation results.
RequirementsThe STRUCTURE program.
Installation and Usage
A manual is included in the distribution.
Montana, G. and Pritchard J. K. (2004) Statistical tests for admixture mapping with case-control and case-only data. American Journal of Human Genetics. 75:771-789