MALDSoft is a program for admixture mapping of complex trait loci, using case-control data. The samples should come from a recently-admixed; population; additional ‘learning’ samples from the parental populations are helpful.
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Giovanni Montana and Jonathan K. Pritchard, 2004.
Statistical Tests for Admixture Mapping with Case-Control and Cases-Only Data
Am J. Hum Genet. 75:771 -789