title: ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.
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.
  
  
  
  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
  
  
  
  celine.scornavacca@umontpellier.fr
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: ISE-M, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France.
authors.forename: Edwin
authors.initials: E
authors.lastname: Jacox
authors.affiliation: Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
authors.forename: Cedric
authors.initials: C
authors.lastname: Chauve
authors.affiliation: ELTE-MTA "Lendület" Biophysics Research Group, Budapest, Hungary.
authors.forename: Gergely J
authors.initials: GJ
authors.lastname: Szöllősi
authors.affiliation: LIX, CNRS/Inria AMIB, Ecole Polytechnique, Palaiseau, France.
authors.forename: Yann
authors.initials: Y
authors.lastname: Ponty
authors.affiliation: ISE-M, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France Institut de Biologie Computationnelle (IBC), Montpellier, France.
authors.forename: Celine
authors.initials: C
authors.lastname: Scornavacca
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D020440:Gene Duplication; D008962:Models, Theoretical; D005810:Multigene Family; D010802:Phylogeny