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An Improved Algorithm for the Macro-evolutionary Phylogeny Problem

  • Behshad Behzadi
  • Martin Vingron
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4009)

Abstract

Macro-evolutionary processes (e.g., gene duplication and loss) have rarely been incorporated into gene phylogeny reconstruction methods. Durand et al. [5] have proposed a polynomial time dynamic programming algorithm to find the gene family tree that optimizes a macro-evolutionary criterion which is the weighted sum of the number of gene duplications and losses. The complexity of this algorithm is O(nm 2) where n is the number of species and m is the maximum number of copies of the gene in a species. In this paper, we propose an improved algorithm with time complexity of O(nm) for solving this problem. We also show, that the problem can be solved in O(n) if unit costs are considered for both loss and duplication.

Keywords

Species Tree Gene Duplication Gene Tree Improve Algorithm Optimal Interval 
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

  • Behshad Behzadi
    • 1
  • Martin Vingron
    • 1
  1. 1.Computational Molecular Biology DepartmentMax Planck Institute for Molecular GeneticsBerlinGermany

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