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Bioinformatics. 2016 Jul 1;32(13):2056-8. doi: 10.1093/bioinformatics/btw105. Epub 2016 Feb 26.

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.

Author information

1
ISE-M, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France.
2
Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
3
ELTE-MTA "Lendület" Biophysics Research Group, Budapest, Hungary.
4
LIX, CNRS/Inria AMIB, Ecole Polytechnique, Palaiseau, France.
5
ISE-M, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France Institut de Biologie Computationnelle (IBC), Montpellier, France.

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.

AVAILABILITY AND IMPLEMENTATION:

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

CONTACT:

celine.scornavacca@umontpellier.fr

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27153713
DOI:
10.1093/bioinformatics/btw105
[Indexed for MEDLINE]

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