jModelTest: phylogenetic model averaging.

By David Posada. Molecular biology and evolution, 2008

10,549 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/694485807b355f7073757b740fd905340ae2f0b7

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Citations in the corpus

bModelTest: Bayesian phylogenetic site model averaging and model comparison (2015, methodology): “A common approach is to use a likelihood-based method like ModelTest [1], jModelTest [2], or jModel-Test2 [3] to determine the site model .”
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space (2012, methodology): “It is standard practice today to select a substitution model for Bayesian phylogenetic inference using a priori model selection procedures (Goldman 1993; Posada 1998, 2008; Suchard et al. 2001).”
Hymenochaetaceae (Basidiomycota) in China (2010, methodology): “Colour terms follow Rayner (1970) and Petersen (1996).”
Revealing secret liaisons: DNA barcoding changes our understanding of food webs (2010, methodology): “Evolutionary models for the Bayesian analyses were identified using the procedure JModelTest (Posada, 2008), and a GTR+I+G model of sequence evolution was applied for mitochondrial sequences of C.”
New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha) (2014, methodology): “…schemes: (1) nine separate partitions, one for each of the individual loci, with each locus being assigned the GTR+G model, selected by jModeltest (Posada, 2008) as the best model with the only exception in COI, for which modeltest selected HKY+G (Hasegawa et al., 1985); (2) seven separate…”
Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea (2012, methodology): “1 (Guindon & Gascuel 2003; Posada 2008), a GTR+I+G model was applied to each partition.”
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models (2019, methodology): “Not surprisingly, a number of bioinformatic tools have been developed in the last 20 years for selecting the best-fit model for the data at hand (Posada and Crandall 1998; Posada 2008; Darriba et al. 2011, 2012; Kalyaanamoorthy et al. 2017).”
A molecular phylogeny and new subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae) (2014, methodology): “Nucleotide substitution models selected by Akaike’s information criterion, as implemented in jModelTest v.0.1.1 (Posada, 2008), were specified for each partition (Table 1).”
A taxonomic revision of Phytophthora Clade 5 including two new species, Phytophthora agathidicida and P. cocois (2015, methodology): “4 (Posada 2008) was used to carry out statistical selection of best-fit models of nucleotide substitution using the corrected Akaike information criteria (AICc).”
Endophytic species of Colletotrichum associated with mango in northeastern Brazil (2014, methodology): “Bayesian phylogenetic estimates were inferred with MrBayes v. 3.2.1 (Ronquist et al. 2012) using the best-fit models of nucleotide substitution selected by jModelTest v. 0.1.1 (Posada 2008) for each loci with the Bayesian Information Criterion (BIC) (Table 2).”
Sensitivity and Specificity of Information Criteria (2018, neutral): “The AIC and BIC are widely used in many important applications in bioinformatics, including in molecular phylogenetics (Posada, 2008; Darriba et al., 2012; Jayaswal et al., 2014; Kalyaanamoorthy et al., 2017; Lefort et al., 2017).”
Molecular taxonomy and naming of five cryptic species of Alviniconcha snails (Gastropoda: Abyssochrysoidea) from hydrothermal vents (2015, positive): “JMODELTEST with the BIC selection criterion (Darriba, Taboada, Doallo, & Posada, 2012; Guindon & Gascuel, 2003; Posada, 2008).”