TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees
Marina Marcet-Houben and Toni Gabaldón*
Author Affiliations
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), UPF, Doctor Aiguader, 88, 08003 Barcelona, Spain
*To whom correspondence should be addressed. Tel: +34 933160281; Fax: +34 93 3969983; Email: tgabaldon@crg.es
Received June 14, 2010.
Revision received February 2, 2011.
Accepted February 3, 2011.
Abstract
Comparisons of tree topologies provide relevant information in evolutionary studies. Most existing methods share the drawback of requiring a complete and exact mapping of terminal nodes between the compared trees. This severely limits the scope of genome-wide analyses, since trees containing duplications are pruned arbitrarily or discarded. To overcome this, we have developed treeKO, an algorithm that enables the comparison of tree topologies, even in the presence of duplication and loss events. To do so treeKO recursively splits gene trees into pruned trees containing only orthologs to subsequently compute a distance based on the combined analyses of all pruned tree comparisons. In addition treeKO, implements the possibility of computing phylome support values, and reconciliation-based measures such as the number of inferred duplication and loss events.
© The Author(s) 2011. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License
(http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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