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Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

Caporaso, J Gregory; Smit, Sandra; Easton, Brett; Hunter, Lawrence; Huttley, Gavin Austin


BACKGROUND: Identifying coevolving positions in protein sequences has myriad applications, ranging from understanding and predicting the structure of single molecules to generating proteome-wide predictions of interactions. Algorithms for detecting coevolving positions can be classified into two categories: tree-aware, which incorporate knowledge of phylogeny, and tree-ignorant, which do not. Tree-ignorant methods are frequently orders of magnitude faster, but are widely held to be...[Show more]

CollectionsANU Research Publications
Date published: 2008-12-03
Type: Journal article
Source: BMC Evolutionary Biology
DOI: 10.1186/1471-2148-8-327


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