Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve (1) , Yann Ponty (2, 3, 4) , João Paulo Pereira Zanetti (5, 6)

1 SFU - Department of Mathematics [Burnaby]
2 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
3 AMIB - Algorithms and Models for Integrative Biology
4 PIMS SFU - Pacific institute for the Mathematical Science (SFU)
5 IC - Institute of Computing [Campinas]
6 Sao Paulo Research Foundation

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.

Mots clés: Dynamic Programming; Boltzmann Ensemble; Syntheny; Reconciliation; Phylogenies

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

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⟩