An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers

Authors:
Jean-Philippe Doyon;Celine Scornavacca;K. Yu Gorbunov;Gergely J. Szöllösi;Vincent Ranwez;Vincent Berry
Affiliations:
LIRMM, CNRS, Univ. Montpellier 2, France;Center for Bioinformatics, Tuebingen Univ., Germany;Kharkevich IITP, Russian Academy of Sciences, Moscow;LBBE, CNRS, Univ. Lyon 1, France;ISEM, CNRS, Univ. Montpellier 2, France;LIRMM, CNRS, Univ. Montpellier 2, France
Venue:
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Year:
2010

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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.