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Haplotype phase inference software tools | Population genetics data analysis

Haplotype phase inference software tools | Population genetics data analysis

Two categories of computational methods exist for determining haplotypes: haplotype phasing and haplotype assembly. Given the genotypes of a sample of individuals from a population, haplotype phasing attempts to infer the haplotypes of the sample using haplotype sharing information within the sample. In the related problem of genotype imputation, a phased reference panel is used to infer missing markers and haplotype phase of the sample (Marchini and Howie, 2010). Methods for haplotype phasing and imputation are based on computational (Halldórsson et al., 2004) and statistical inference (Browning and Browning, 2011) techniques, but both use the fact that closely spaced markers tend to be in linkage disequilibrium and smaller haplotypes blocks are often shared in a population of seemingly unrelated individuals. Source text: Aguiar and Istrail, 2012.

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