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Bioinformatics Advance Access originally published online on October 18, 2005
Bioinformatics 2006 22(1):117-119; doi:10.1093/bioinformatics/bti720
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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A novel algorithm and web-based tool for comparing two alternative phylogenetic trees

Tom M.W. Nye 1,*, Pietro Liò 2 and Walter R. Gilks 1

1Medical Research Council Biostatistics Unit Cambridge, UK
2University of Cambridge Computer Laboratory Cambridge, UK

*To whom correspondence should be addressed.

Summary: We describe an algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score. The software enables the user to explore the corresponding mapping between the phylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length.

Availability: The software is implemented as a Java applet at http://www.mrc-bsu.cam.ac.uk/personal/thomas/phylo_comparison/comparison_page.html. It is also available on request from the authors.

Contact: thomas.nye{at}mrc-bsu.cam.ac.uk

Received on August 15, 2005; revised on September 28, 2005; accepted on October 14, 2005

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