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MBE Advance Access published online on December 29, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi074
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.
Accepted December 21, 2004

Research Article

Listening to Viral Tongues: Comparing Viral Trees Using a Stochastic Context-Free Grammar

Andrey Rzhetsky 1 and Walter M. Fitch 2*

1 Department of Biomedical Informatics, Columbia Genome Center, and Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY 10032
2 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697

* To whom correspondence should be addressed.
Walter M. Fitch, E-mail: wfitch{at}uci.edu


  Abstract

We suggest a probabilistic method for comparing the topological features of large phylogenetic trees. Using this method, we demonstrate that a stochastic grammar can generate three influenza-subtype (A H1, A H3, and B) hemagglutinin trees used in an earlier study, with statistically similar parameters. The proposed methodology is applicable to a broad class of problems that require comparison of the topological properties of various dendrograms.

Keywords: stochastic context-free grammar; human influenza virus hemagglutinin; stochastic measures of tree similarity; multitype branching processes.
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