Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models - PubMed (original) (raw)

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

Art F Y Poon et al. Bioinformatics. 2008.

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.

Availability: 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.

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Figures

Fig. 1.

Flowchart diagram of the Spidermonkey pipeline. Abbreviations: SLAC=single likelihood ancestor counting; FEL=fixed effects likelihood; IFEL=internal FEL; REL=random effects likelihood (Kosakovsky Pond and Frost, 2005c); PARRIS=a partitioning approach for robust inference of selection (Scheffler et al., 2006); GA-Branch=genetic algorithm for detecting branch-specific selection (Kosakovsky Pond and Frost, 2005b).

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Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models - PubMed (original) (raw)