Journal Article10.1146/ANNUREV.ECOLSYS.36.102003.152633
Model Selection in Phylogenetics
Jack Sullivan,Paul Joyce +1 more
TL;DR: Issues that render model-based approaches necessary are reviewed, nucleotide-based models that attempt to capture relevant features of evolutionary processes are briefly reviewed, and methods that have been applied to model selection in phylogenetics are reviewed: likelihood-ratio tests, AIC, BIC, and performance- based approaches.
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Abstract: ▪ Abstract Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches.
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jModelTest 2: more models, new heuristics and parallel computing.
TL;DR: jModelTest 2: more models, new heuristics and parallel computing Diego Darriba, Guillermo L. Taboada, Ramón Doallo and David Posada.
jModelTest: Phylogenetic Model Averaging
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
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References
•Book
Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach
Kenneth P. Burnham,David E. Anderson +1 more
- 19 Jun 2013
TL;DR: The second edition of this book is unique in that it focuses on methods for making formal statistical inference from all the models in an a priori set (Multi-Model Inference).
45.1K
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
Gideon Schwarz
- 01 Jan 2005
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.
40.6K
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
29K
MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
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