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Bioinformatics Advance Access published online on June 18, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn313
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models

Art F. Y. Poon 1,*, Fraser I. Lewis 2, Simon D. W. Frost 1 and Sergei L. Kosakovsky Pond 1

1 Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, CA, 92103, USA.
2 Epidemiology Research Unit, Scottish Agricultural College, Inverness, Scotland, IV2 4JZ, UK.

*To whom correspondence should be addressed. Dr. Art F. Y. Poon, E-mail: afpoon{at}ucsd.edu


  Abstract

Spidermonkey is a new component of the Datamonkey suite of phylogenetic tools that provides methods for detecting co-evolving sites from a multiple alignment of homologous nucleotide or amino acid sequences. It reconstructs the substitution history of the alignment by maximum likelihood-based phylogenetic methods, and then analyzes the joint distribution of substitution events using Bayesian graphical models to identify significant associations among sites.

Availability: Spidermonkey is publicly available both as a web application at http://www.datamonkey.org and as a stand-alone component of the phylogenetic software package HyPhy, which is freely distributed on the web (http://www.hyphy.org) as precompiled binaries and open source.

Contact: afpoon{at}ucsd.edu

Associate Editor: Prof. Alfonso Valencia

Received on April 15, 2008; revised on June 6, 2008; accepted on June 15, 2008

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