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
CNRS - Centre National de la Recherche Scientifique : UMR8623, X - École polytechnique, Inria Saclay - Ile de France, UP11 - Université Paris-Sud - Paris 11, LRI - Laboratoire de Recherche en Informatique, LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
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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Article dans une revue
BMC Bioinformatics, BioMed Central, 2015, 16 (Suppl 19), pp.S6. 〈http://www.biomedcentral.com/1471-2105/16/S19/S6〉. 〈10.1186/1471-2105-16-S19-S6〉
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https://hal.inria.fr/hal-01245495
Contributeur : Yann Ponty <>
Soumis le : jeudi 17 décembre 2015 - 12:24:46
Dernière modification le : jeudi 10 mai 2018 - 02:06:07

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Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics, BioMed Central, 2015, 16 (Suppl 19), pp.S6. 〈http://www.biomedcentral.com/1471-2105/16/S19/S6〉. 〈10.1186/1471-2105-16-S19-S6〉. 〈hal-01245495〉

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