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

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Abstract
Spidermonkey is a new component of the Datamonkey suite of phylogenetic tools that provides methods for detecting coevolving 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. Spidermonkey is publicly available both as a web application at http://www.data-monkey.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.