SMS: Smart Model Selection in PhyML - LIRMM - Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier Access content directly
Journal Articles Molecular Biology and Evolution Year : 2017

SMS: Smart Model Selection in PhyML


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 (
Fichier principal
Vignette du fichier
msx149.pdf (456.02 Ko) Télécharger le fichier
Origin : Files produced by the author(s)

Dates and versions

lirmm-01794206 , version 1 (13-03-2019)


Attribution - NonCommercial



Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel. SMS: Smart Model Selection in PhyML. Molecular Biology and Evolution, 2017, 34 (9), pp.2422-2424. ⟨10.1093/molbev/msx149⟩. ⟨lirmm-01794206⟩
331 View
156 Download



Gmail Facebook X LinkedIn More