Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution

By David Posada. Current Protocols in Bioinformatics, 2003

353 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/17b1cae16a1060c4587efb920fd461e498e3b01e

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In Molecular Biology

1. T. Buckley
2. C. Lejeusne
3. P. Chevaldonné
4. J. Ivanisevic
5. T. Pérez
6. O. Thomas
7. Gane Ka-Shu Wong
8. Jun Yu

Citations in the corpus

• KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging (2007, methodology): “We focused on a set of time-reversible substitution models ( 9–16 ) as shown in Table 1 ( 17 , 18 ), ranging from the Jukes-Cantor (JC) model, which assumes that all substitutions have equal rates and equal nucleotide frequencies, to the general time-reversible (GTR) model that considers six…”
• ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online (2006, background): “Further instructions can be found in the program manual (also available from the help page of the server) or in (6,7).”
• Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data (2011, neutral): “1985) 4 AC1⁄4AT1⁄4CG1⁄4GT, AG1⁄4CT TN93ef 2 TN93 (Tamura & Nei 1993) 5 AC1⁄4AT1⁄4CG1⁄4GT, AG, CT K81* (Kimura 1981) 2 K81uf* 5 AC1⁄4GT, AT1⁄4CG, AG1⁄4CT J1ef 3 J1 (Jobb 2008) 6 AC1⁄4CG, AT1⁄4GT, AG, CT J2ef 3 J2 (Jobb 2008) 6 AC1⁄4AT, CG1⁄4GT, AG, CT TIMef 3 TIM (Posada 2003) 6 AC1⁄4GT, AT1⁄4CG, AG,”
• Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. (2004, methodology): “As discussed above, model averaging can also be applied to the estimation of phylogenetic trees (Posada, 2003).”
• Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. (2004, neutral): “Downloaded from https://academic.oup.com/mbe/article-abstract/21/6/1123/1050772 by guest on 28 July 2018 Nei 1993), 123321 (Kimura 1981), 123341 (Posada 2003), 123425 (Posada 2003), and 123456 (Tavaré 1986).”
• Metabolic fingerprinting as an indicator of biodiversity: towards understanding inter-specific relationships among Homoscleromorpha sponges (2011, methodology): “The Akaike Information Criterion was used in jMODELTEST (Posada 2008) to determine the best-fit model of nucleotide substitution, which was the ‘‘transitional model’’ (Posada 2003) with a proportion of invariable sites and gamma correction (TIM2 ? I ? G).”
• bModelTest: Bayesian phylogenetic site model averaging and model comparison (2015, neutral): “Alternatively, if one is interested in using named models, we can restrict further to include only Jukes Cantor [18, 19] (111,111), HKY [15] (121,121), TN93 [20] (121,131), K81 [21] (123,321), TIM [22] (123,341), TVM [22] (123,425),and GTR [14] (123,456).”