Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection

We consider three approaches for estimating the rates of nonsynonymous and synonymous changes at each site in a sequence alignment in order to identify sites under positive or negative selection: (1) a suite of fast likelihood-based "counting methods" that employ either a single most likely ancestral reconstruction, weighting across all possible ancestral reconstructions, or sampling from ancestral reconstructions; (2) a random effects likelihood (REL) approach, which models variation in nonsynonymous and synonymous rates across sites according to a predefined distribution, with the selection pressure at an individual site inferred using an empirical Bayes approach; and (3) a fixed effects likelihood (FEL)…

• UO
  University of Edinburgh
• NI
  National Institutes of Health
• CF
  Center for AIDS Research, University of Washington
• NI
  National Institute of Allergy and Infectious Diseases