HAPAA is a novel approach for ancestry inference that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy.
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Genome Res. 2008 Apr;18(4):676-82. doi: 10.1101/gr.072850.107.
Effect of genetic divergence in identifying ancestral origin using HAPAA.
Sundquist A, Fratkin E, Do CB, Batzoglou S.