ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony - Laboratoire d'informatique de l'école polytechnique Accéder directement au contenu
Article Dans Une Revue Bioinformatics Année : 2016

ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony

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
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.
Fichier principal
Vignette du fichier
Scornavacca_24.pdf (169.71 Ko) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)
Loading...

Dates et versions

hal-01276903 , version 1 (16-12-2019)

Identifiants

Citer

Edwin Jacox, Cedric Chauve, Gergely J Szöllősi, Yann Ponty, Celine Scornavacca. ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics, 2016, 32 (13), pp.2056-2058. ⟨10.1093/bioinformatics/btw105⟩. ⟨hal-01276903⟩
622 Consultations
312 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More