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Inferring the ancestral origin of chromosomal segments in admixed individuals is key for genetic applications, ranging from analyzing population demographics and history, to mapping disease genes. Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes. In this paper we introduce ALLOY, an efficient method that incorporates generalized, but highly expressive, linkage disequilibriumdoi:10.1089/cmb.2012.0088 pmid:23421795 pmcid:PMC3590892 fatcat:v2zs5cl4urf6jg6hr3o6nodljq