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


BACKGROUND
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.
Poon
Art F Y
AF
Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, CA 92103, USA. afpoon@ucsd.edu
Lewis
Fraser I
FI
Frost
Simon D W
SD
Kosakovsky Pond
Sergei L
SL
D000595:Amino Acid Sequence; D001483:Base Sequence; D001499:Bayes Theorem; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D019143:Evolution, Molecular; D008956:Models, Chemical; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D017421:Sequence Analysis / Q000379:methods*; D012984:Software
D011506:Proteins; D004247:DNA