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ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony

Edwin Jacox 1 Cedric Chauve 2 Gergely J Szöllősi 3 Yann Ponty 4 Celine Scornavacca 1
4 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
Résumé : A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation, involving sampled and unsampled lineages, within undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize or improve upon most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species-tree aware gene trees using amalgamation. ecceTERA is freely available under http://mbb.univ-montp2.fr/MBB/download_sources/16__ecceTERA and can be run online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera
Abstract : A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss, and transfer (DTL) as well as speciation, involving sampled and unsampled lineages, within undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize or improve upon most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species-tree aware gene trees using amalgamation.
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Edwin Jacox, Cedric Chauve, Gergely J Szöllősi, Yann Ponty, Celine Scornavacca. ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics, Oxford University Press (OUP), 2016, 32 (13), pp.2056-2058. ⟨10.1093/bioinformatics/btw105⟩. ⟨hal-01276903⟩

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