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1 Department of Mathematics Burnaby 2 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, Polytechnique - X, CNRS - Centre National de la Recherche Scientifique : UMR8623 3 LIX - Laboratoire d-informatique de l-École polytechnique Palaiseau

Abstract : The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by Bérard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. Following the approach pioneered by Sturmfels and Pachter, we describe how to modify the DeCo dynamic programming algorithm to identify classes of cost schemes that generates similar parsimonious evolutionary scenarios for gene adjacencies, as well as the robustness to changes to the cost scheme of evolutionary events of the presence or absence of specific ancestral gene adjacencies. We apply our method to six thousands mammalian gene families, and show that computing the robustness to changes to cost schemes provides new and interesting insights on the evolution of gene adjacencies and the DeCo model.

Keywords : Parsimony Evolution Parametric Algorithms Synteny Dynamic Programming





Autor: Ashok Rajaraman - Cedric Chauve - Yann Ponty -

Fuente: https://hal.archives-ouvertes.fr/



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