SMS: Smart Model Selection in PhyML.
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TLDR
The 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/).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/).read more
Citations
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Journal ArticleDOI
ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models
Diego Darriba,David Posada,Alexey M. Kozlov,Alexandros Stamatakis,Alexandros Stamatakis,Benoit Morel,Tomas Flouri +6 more
TL;DR: ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively, and introduces several new features, such as ascertainment bias correction, mixture, and free-rate models, or the automatic processing of single partitions.
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Genomic evidence for reinfection with SARS-CoV-2: a case study.
Richard L. Tillett,Richard L. Tillett,Joel Sevinsky,Paul D. Hartley,Heather Kerwin,Natalie Crawford,Andrew Gorzalski,Chris Laverdure,Subhash C. Verma,Cyprian C. Rossetto,David Jackson,Megan J Farrell,Stephanie Van Hooser,Mark Pandori +13 more
TL;DR: The findings suggest that the patient was infected by SARS-CoV-2 on two separate occasions by a genetically distinct virus, suggesting that previous exposure to Sars-Cov-2 might not guarantee total immunity in all cases.
Posted ContentDOI
ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models
Diego Darriba,David Posada,Alexey M. Kozlov,Alexandros Stamatakis,Alexandros Stamatakis,Benoit Morel,Tomas Flouri +6 more
TL;DR: ModelTest-NG is a re-implementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively, and introduces several new features, such as ascertainment bias correction, mixture and FreeRate models, or the automatic processing of partitioned datasets.
Journal ArticleDOI
Sensitivity and specificity of information criteria.
TL;DR: In some cases the comparison of two models using ICs can be viewed as equivalent to a likelihood ratio test, with the different criteria representing different alpha levels and BIC being a more conservative test than AIC.
Journal ArticleDOI
Renewing Felsenstein’s phylogenetic bootstrap in the era of big data
Frédéric Lemoine,Jean-Baka Domelevo Entfellner,Eduan Wilkinson,Damien Correia,M. Davila Felipe,T. de Oliveira,Olivier Gascuel +6 more
TL;DR: A new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual ‘transfer’ distance rather than the binary presence or absence index used in Felsenstein’s original version is proposed.
References
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Journal ArticleDOI
Estimating the Dimension of a Model
TL;DR: In this paper, the problem of selecting one of a number of models of different dimensions is treated by finding its Bayes solution, and evaluating the leading terms of its asymptotic expansion.
Estimating the dimension of a model
TL;DR: In this paper, the problem of selecting one of a number of models of different dimensions is treated by finding its Bayes solution, and evaluating the leading terms of its asymptotic expansion.
Journal ArticleDOI
MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
Proceedings Article
Information Theory and an Extention of the Maximum Likelihood Principle
TL;DR: The classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion to provide answers to many practical problems of statistical model fitting.
Journal ArticleDOI
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Stéphane Guindon,Jean-François Dufayard,Vincent Lefort,Maria Anisimova,Wim Hordijk,Olivier Gascuel +5 more
TL;DR: A new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves and a new test to assess the support of the data for internal branches of a phylogeny are introduced.
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