An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model

  • Aïda Ouangraoua
  • Krister M. Swenson
  • Cedric Chauve
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6398)

Abstract

We consider the following problem: given a forest of gene family trees on a set of genomes, find a first speciation which splits these genomes into two subsets and minimizes the number of gene duplications that happened before this speciation. We call this problem the Minimum Duplication Bipartition Problem. Using a generalization of the Minimum Edge-Cut Problem, known as Submodular Function Minimization, we propose a polynomial time and space 2-approximation algorithm for the Minimum Duplication Bipartition Problem. We illustrate the potential of this algorithm on both synthetic and real data.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Aïda Ouangraoua
    • 1
    • 2
    • 3
  • Krister M. Swenson
    • 2
    • 4
  • Cedric Chauve
    • 1
    • 2
  1. 1.Department of MathematicsSFUBurnabyCanada
  2. 2.LacimUniversité du Québec à MontréalMontréalCanada
  3. 3.INRIA LNE, LIFLUniversité Lille 1France
  4. 4.Department of Mathematics and StatisticsUniversity of OttawaOttawaCanada

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