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Phylogeny- and Parsimony-Based Haplotype Inference with Constraints

  • Michael Elberfeld
  • Till Tantau
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6129)

Abstract

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. In their cpm 2009 paper, Fellows et al. studied an extension of this approach that incorporates prior knowledge in the form of a set of candidate haplotypes from which the right haplotypes must be chosen. While this approach may help to increase the accuracy of haplotyping methods, it was conjectured that the resulting formal problem constrained perfect phylogeny haplotyping might be NP-complete. In the present paper we present a polynomial-time algorithm for it. Our algorithmic ideas also yield new fixed-parameter algorithms for related haplotyping problems based on the maximum parsimony assumption.

Keywords

Maximum Parsimony Recursive Call Distinct Haplotype Phase Constraint Haplotype Inference 
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 2010

Authors and Affiliations

  • Michael Elberfeld
    • 1
  • Till Tantau
    • 1
  1. 1.Institut für Theoretische InformatikUniversität zu LübeckLübeckGermany

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