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Topological Rearrangements and Local Search Method for Tandem Duplication Trees

  • Denis Bertrand
  • Olivier Gascuel
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)

Abstract

The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent works deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees (DT). In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on DT. We demonstrate that restricting the neighborhood defined by the SPR (Subtree Pruning and Re-grafting) rearrangement to valid duplication trees, allows exploring the whole space of DT. We use these restricted rearrangements in a local search method which improves an initial tree via successive rearrangements and optimizes the parsimony criterion. We show through simulations that this method improves all existing programs for both reconstructing the initial tree and recovering its duplication events.

Keywords

Local Search Duplication Event Internal Node Local Search Method Clock Tree 
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 2004

Authors and Affiliations

  • Denis Bertrand
    • 1
  • Olivier Gascuel
    • 1
  1. 1.Equipe Méthodes et Algorithmes pour la Bioinformatique LIRMM-CNRSMontpellier Cedex 5France

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