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

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. © The Author 2008. Published by Oxford University Press. All rights reserved.