SMS: Smart Model Selection in PhyML
By Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel. Molecular biology and evolution, 2017
1,652 citations recorded by the source corpus.
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/).
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/ed2a53540f6dfc4332cd4511352b6301d162f21a
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Genetics
- Alexandros Stamatakis
- Olivier Gascuel
- Vincent Lefort
- Diego Darriba
- David Posada
- Tomás Flouri
- Alexey M. Kozlov
- Damien Correia
In Molecular Biology
- Alexandros Stamatakis
- Olivier Gascuel
- Vincent Lefort
- Diego Darriba
- David Posada
- Tomás Flouri
- Alexey M. Kozlov
- Benoit Morel
Citations in the corpus
- COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning (2020, methodology): “The phylogenetic tree was constructed using PhyML 64 , and the amino acid conservation was estimated by the Jensen-Shannon Divergence (JSD) 65 .”
- ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models (2019, methodology): “Another recently released tool for model selection is SMS (Smart Model Selection) (Lefort et al. 2017).”
- Sensitivity and Specificity of Information Criteria (2018, neutral): “bioinformatics, including in molecular phylogenetics (Posada, 2008; Darriba et al., 43 2012; Jayaswal et al., 2014; Kalyaanamoorthy et al., 2017; Lefort et al., 2017).”
- NGPhylogeny.fr: new generation phylogenetic services for non-specialists (2019, methodology): “The four ‘ One click ’ workflows differ only at the tree inference step, which can be performed by FastTree (22), FastME (4), PhyML (3) or PhyML+SMS (24).”