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Bioinformatics Advance Access published online on September 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm432
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Phylocomposer and Phylodirector: Analysis and Visualization of Transducer Indel Models

Ian Holmes

Department of Bioengineering, University of California, Berkeley CA, USA

*To whom correspondence should be addressed. Dr. Ian Holmes, E-mail: ihh{at}berkeley.edu


  Abstract

Summary: Finite-state string transducers are probabilistic tools similar to Hidden Markov Models that can be systematically extended to large numbers of sequences related by indel and substitutionprocesses on phylogenetic trees. The number of states in such models grows exponentially with the number of nodes in the tree, with the consequence that even quite small trees can be difficult to analyze or visualize. Here, we present two tools, phylocomposer and phylodirector, for working with string transducers. The former tool implements previously described composition algorithms for extending transducers to arbitrary tree topologies, while the latter generates short animations for arbitrary input alignments and phylogenetic trees, illustrating the state path through the composed transducer.

Availability: phylocomposer and phylodirector are freely available at http://biowiki.org/PhyloComposer and http://biowiki.org/PhyloDirector

Contact: ihh{at}berkeley.edu

Associate Editor: Prof. Martin Bishop

Received on April 9, 2007; revised on August 1, 2007; accepted on August 17, 2007

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