Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model.

ABSTRACT: The relative evolutionary rates at individual sites in proteins are informative measures of conservation or adaptation. Often used as evolutionarily aware conservation scores, relative rates reveal key functional or strongly selected residues. Estimating rates in a phylogenetic context requires specifying a protein substitution model, which is typically a phenomenological model trained on a large empirical data set. A strong emphasis has traditionally been placed on selecting the "best-fit" model, with the implicit understanding that suboptimal or otherwise ill-fitting models might bias inferences. However, the pervasiveness and degree of such bias has not been systematically examined. We investigated how model choice impacts site-wise relative rates in a large set of empirical protein ali

SUBMITTER: Spielman SJ 

PROVIDER: S-EPMC6107055 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature