Title: A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
Authors: Lemey, Philippe ×
Minin, Vladimir N
Bielejec, Filip
Kosakovsky Pond, Sergei L
Suchard, Marc A #
Issue Date: Dec-2012
Publisher: Oxford University Press
Series Title: Bioinformatics vol:28 issue:24 pages:3248-3256
Article number: 10.1093/bioinformatics/bts580
Abstract: Statistical methods for comparing relative rates of synonymous and non-synonymous substitutions maintain a central role in detecting positive selection. To identify selection, researchers often estimate the ratio of these relative rates ( ) at individual alignment sites. Fitting a codon substitution model that captures heterogeneity in across sites provides a reliable way to perform such estimation, but it remains computationally prohibitive for massive datasets. By using crude estimates of the numbers of synonymous and non-synonymous substitutions at each site, counting approaches scale well to large datasets, but they fail to account for ancestral state reconstruction uncertainty and to provide site-specific estimates.
ISSN: 1367-4803
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Clinical and Epidemiological Virology (Rega Institute)
× corresponding author
# (joint) last author

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