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Bioinformatics Advance Access published online on September 22, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm466
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees

Víctor Soria-Carrasco , Gerard Talavera , Javier Igea and Jose Castresana *

Department of Physiology and Molecular Biodiversity, Institute of Molecular Biology of Barcelona, CSIC, Jordi Girona 18, 08034 Barcelona, Spain

*To whom correspondence should be addressed. Dr. Jose Castresana, E-mail: jcvagr{at}ibmb.csic.es


  Abstract

Summary: We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length varia-tion. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree.

Availability: http://molevol.ibmb.csic.es/Ktreedist.html

Contact: jcvagr{at}ibmb.csic.es

Associate Editor: Prof. Keith Crandall

Received on June 26, 2007; revised on August 13, 2007; accepted on September 6, 2007

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