Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models

  title={Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models},
  author={Sivan Bercovici and Jesse M. Rodriguez and Megan Elmore and Serafim Batzoglou},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  volume={20 3},
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 disequilibrium models… 

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