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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Bibliographic Details
Published in:Journal of computational biology Vol. 17; no. 10; p. 1451
Main Authors: Doan, Duong D, Evans, Patricia A, Horton, Joseph D
Format: Journal Article
Language:English
Published: United States 01.10.2010
Subjects:
Algorithms
Haplotypes
Models, Genetic
Pedigree
ISSN:1557-8666, 1557-8666
Online Access:Get more information
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Summary: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