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Nucleic Acids Res. 2011 May;39(10):e66. doi: 10.1093/nar/gkr087. Epub 2011 Feb 18.

TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.

Author information

1
Centre for Genomic Regulation, UPF, Doctor Aiguader 88, 08003 Barcelona, Spain.

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.

PMID:
21335609
PMCID:
PMC3105381
DOI:
10.1093/nar/gkr087
[Indexed for MEDLINE]
Free PMC Article

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