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Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve 1 Yann Ponty 2, 3 João Paulo Pereira Zanetti 4 
3 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : CONTEXT:The reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Berard et al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered.CONTRIBUTION:We extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies.RESULTS:We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies.
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Submitted on : Thursday, December 17, 2015 - 12:24:46 PM
Last modification on : Tuesday, October 25, 2022 - 4:19:54 PM

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Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics, 2015, 16 (Suppl 19), pp.S6. ⟨10.1186/1471-2105-16-S19-S6⟩. ⟨hal-01245495⟩



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