MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
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The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.Abstract:
Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.read more
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MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space
Fredrik Ronquist,Maxim Teslenko,Paul van der Mark,Daniel L. Ayres,Aaron E. Darling,Sebastian Höhna,Bret Larget,Liang Liu,Marc A. Suchard,John P. Huelsenbeck +9 more
TL;DR: The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
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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.
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jModelTest: Phylogenetic Model Averaging
TL;DR: jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" that implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion", the "Bayesian information criterion," and a "decision-theoretic performance-based" approach.
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ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy,Subha Kalyaanamoorthy,Bui Quang Minh,Thomas K. F. Wong,Thomas K. F. Wong,Arndt von Haeseler,Arndt von Haeseler,Lars S. Jermiin,Lars S. Jermiin +8 more
TL;DR: ModelFinder is presented, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
References
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Journal ArticleDOI
Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood
TL;DR: The maximum likelihood method is described and how likelihood ratio tests of a variety of biological hypotheses can be formulated and tested using computer simulation to generate the null distribution of the likelihood ratio test statistic is described.
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Statistical tests of models of DNA substitution
TL;DR: A test statistics suggested by Cox is employed to test the adequacy of some statistical models of DNA sequence evolution used in the phylogenetic inference method introduced by Felsentein.
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Estimation of evolutionary distances between nucleotide sequences
TL;DR: A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process by using matrix algebra theory, and it was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 2:191–210, 1987) and Lanave and Hartigan's (Stat. Sci. Sci.) methods are preferable to others for the purpose of phylogenetic analysis when the sequences are long.
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Phylogeny and molecular evolution in primates.
TL;DR: An application of statistical methods to data from primates suggests that chimpanzee is the closest relative of man, and further suggests that these two species diverged about 4-5 million years ago.