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

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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Eric Tannier. RECOMB'10: Comparative Genomics, Oct 2010, Ottawa, Canada. Springer Berlin Heidelberg, 6398 (6398), pp.93-108, 2010, LNCS. 〈http://recombcg.uottawa.ca/recombcg2010/〉. 〈10.1007/978-3-642-16181-0_9〉
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Jean-Philippe Doyon, Celine Scornavacca, Yu Gorbunov, Gergely Szöllősi, Vincent Ranwez, et al.. An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers. Eric Tannier. RECOMB'10: Comparative Genomics, Oct 2010, Ottawa, Canada. Springer Berlin Heidelberg, 6398 (6398), pp.93-108, 2010, LNCS. 〈http://recombcg.uottawa.ca/recombcg2010/〉. 〈10.1007/978-3-642-16181-0_9〉. 〈lirmm-00818889〉

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