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Sampling among haplotype resolutions in a coalescent‐based genealogy sampler
Author(s) -
Kuhner Mary K.,
Felsenstein Joseph
Publication year - 2000
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/1098-2272(2000)19:1+<::aid-gepi3>3.0.co;2-v
Subject(s) - coalescent theory , haplotype , population , biology , genetics , haplotype estimation , evolutionary biology , computational biology , phylogenetics , gene , genotype , demography , sociology
Analysis of the coalescent structure of a population may provide information useful in mapping disease loci. Current coalescent‐based genealogy samplers require haplotyped data, but haplotypes are not always available, and it is not practical to sum over all haplotype assignments for large data sets. We describe a method of adding haplotype re‐evaluation to the sampler, so that it samples not only among genealogies explaining a given haplotype configuration, but also among different haplotype configurations. Several different haplotype‐rearrangement strategies are considered, but the simplest—investing the phase of a single site in a single individual—appears to be the most successful. The straightforward haplotype sampler does not mix well; heating approaches can greatly improve its performance. Genet. Epidemiol. 19(Suppl 1):S15–S21, 2000. © 2000 Wiley‐Liss, Inc.