A near-linear time algorithm for haplotype determination on general pedigrees

Abstract An O(nmα(m)) time algorithm is given for inferring haplotypes from genotypes of non-recombinant pedigree data, where n is the number of members, m is the number of sites, and α(m) is the inverse of the Ackermann function. The algorithm works on both tree and general pedigree structures with...

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Veröffentlicht in:Journal of computational biology Jg. 17; H. 10; S. 1451
Hauptverfasser: Doan, Duong D, Evans, Patricia A, Horton, Joseph D
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States 01.10.2010
Schlagworte:
Algorithms
Haplotypes
Models, Genetic
Pedigree
ISSN:1557-8666, 1557-8666
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Zusammenfassung:Abstract An O(nmα(m)) time algorithm is given for inferring haplotypes from genotypes of non-recombinant pedigree data, where n is the number of members, m is the number of sites, and α(m) is the inverse of the Ackermann function. The algorithm works on both tree and general pedigree structures with cycles. Constraints between pairs of heterozygous sites are used to resolve unresolved sites for the pedigree, enabling the algorithm to avoid problems previously experienced for non-tree pedigrees.
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ISSN:1557-8666
1557-8666
DOI:10.1089/cmb.2009.0133