SMS: Smart Model Selection in PhyML

TLDR

Model selection using likelihood‑based criteria such as AIC is a key initial step in phylogenetic analysis, requiring the choice of both a substitution matrix and a rates‑across‑sites model, traditionally done by exhaustively testing all combinations. The study proposes heuristics to avoid exhaustive calculations in model selection. SMS implements these heuristics in the PhyML environment, offering both a command‑line interface for pipelines and a web server. SMS halves runtime while producing results comparable to ProtTest and jModelTest2.

Abstract

Model selection using likelihood-based criteria (e.g., AIC) is one of the first steps in phylogenetic analysis. One must select both a substitution matrix and a model for rates across sites. A simple method is to test all combinations and select the best one. We describe heuristics to avoid these extensive calculations. Runtime is divided by ∼2 with results remaining nearly the same, and the method performs well compared with ProtTest and jModelTest2. Our software, "Smart Model Selection" (SMS), is implemented in the PhyML environment and available using two interfaces: command-line (to be integrated in pipelines) and a web server (http://www.atgc-montpellier.fr/phyml-sms/).