Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve 1, * Yann Ponty 2, 3, 4, * João Paulo Pereira Zanetti 5, 6
* Corresponding author
1 Department of Mathematics [Burnaby]
2 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
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
4 PIMS SFU - Pacific institute for the Mathematical Science (SFU)
5 UNICAMP - Institute of Computing [Campinas]
6 Sao Paulo Research Foundation
Abstract : We consider a recently introduced dynamic programming scheme to compute parsimonious evolutionary scenarios for gene adjacencies. We extend this scheme to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution. We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic inconsistencies observed in the resulting ancestral gene adjacencies.
Keywords : Phylogenies Reconciliation Syntheny Boltzmann Ensemble Dynamic Programming
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Conference papers
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https://hal.inria.fr/hal-01056140
Contributor : Yann Ponty <>
Submitted on : Tuesday, August 19, 2014 - 11:22:28 PM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM
Long-term archiving on : Tuesday, April 11, 2017 - 7:59:55 PM

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Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BSB - Brazilian Symposium on Bioinformatics - 2014, Oct 2014, Belo Horizonte, Brazil. pp.49--56, ⟨10.1007/978-3-319-12418-6⟩. ⟨hal-01056140v2⟩

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