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Phylogenetic Network Inferences Through Efficient Haplotyping

  • Yinglei Song
  • Chunmei Liu
  • Russell L. Malmberg
  • Liming Cai
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)

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.

Keywords

Directed Acyclic Graph Tree Node Tree Decomposition Phylogenetic Network Incoming Edge 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Yinglei Song
    • 1
  • Chunmei Liu
    • 1
  • Russell L. Malmberg
    • 2
  • Liming Cai
    • 1
  1. 1.Dept. of Computer ScienceUniv. of GeorgiaAthensUSA
  2. 2.Department of Plant BiologyUniversity of GeorgiaAthensUSA

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