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, X - École polytechnique, CNRS - Centre National de la Recherche Scientifique : UMR8623
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
Type de document :
Article dans une revue
Bioinformatics (Oxford, England), 2016, pp.2056-8
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https://hal.inria.fr/hal-01276903
Contributeur : Yann Ponty <>
Soumis le : dimanche 21 février 2016 - 10:22:04
Dernière modification le : jeudi 10 mai 2018 - 02:06:05

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  • HAL Id : hal-01276903, version 1
  • PUBMED : 27153713

Citation

Edwin Jacox, Cedric Chauve, Gergely J Szöllősi, Yann Ponty, Celine Scornavacca. ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.. Bioinformatics (Oxford, England), 2016, pp.2056-8. 〈hal-01276903〉

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