An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers

  • Jean-Philippe Doyon
  • Celine Scornavacca
  • K. Yu. Gorbunov
  • Gergely J. Szöllősi
  • Vincent Ranwez
  • Vincent Berry
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6398)

Abstract

Tree reconciliation methods aim at estimating the evolutionary events that cause discrepancy between gene trees and species trees. We provide a discrete computational model that considers duplications, transfers and losses of genes. The model yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. Then we study the conditions under which parsimony is able to accurately infer such events. Overall, it performs well even under realistic rates, transfers being in general less accurately recovered than duplications. An implementation is freely available at http://www.atgc-montpellier.fr/MPR.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Jean-Philippe Doyon
    • 1
  • Celine Scornavacca
    • 2
  • K. Yu. Gorbunov
    • 3
  • Gergely J. Szöllősi
    • 4
  • Vincent Ranwez
    • 5
  • Vincent Berry
    • 1
  1. 1.LIRMMCNRS - Univ. Montpellier 2France
  2. 2.Center for Bioinformatics (ZBIT)Tuebingen Univ.Germany
  3. 3.Kharkevich IITPRussian Academy of SciencesMoscow
  4. 4.LBBE, CNRS - Univ. Lyon 1France
  5. 5.ISEM, CNRS - Univ. Montpellier 2France

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