ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony

Jacox, Edwin and Chauve, Cedirc and Szöllősi, Gergely J and Ponty, Yann and Scornavacca, Celine (2016) ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony. BIOINFORMATICS. pp. 1-3. ISSN 1367-4803

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Abstract

Summary: 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. Supplementary Information: Supplementary data available online. Availability: ecceTERA is freely available under http://mbb.univ- montp2.fr/MBB/download_sources/16__TERA and can be run online at http://mbb.univ-montp2.fr/MBB/subsection/ softExec.php?soft=eccetera.

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