Phylogenetic network inferences through efficient haplotyping

Abstract

The genotype phasing problem is to determine the haplotypes of diploid individuals from their genotypes where linkage relationships are not known. Based on the model of perfect phylogeny, the genotype phasing problem can be solved in linear time. However, recombinations may occur and the perfect phylogeny model thus cannot interpret genotype data with recombinations. This paper develops a graph theoretical approach that can reduce the problem to finding a subgraph pattern contained in a given graph. Based on ordered graph tree decomposition, this problem can be solved efficiently with a parameterized algorithm. Our tests on biological genotype data showed that this algorithm is extremely efficient and its interpretation accuracy is better than or comparable with that of other approaches. © Springer-Verlag Berlin Heidelberg 2006.