MrBayes 3: Bayesian phylogenetic inference under mixed models

By Fredrik Ronquist, John P. Huelsenbeck. Bioinform., 2003

29,617 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/f256f33b7a0cf35735fba4d5defa2c3da988e490

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Citations in the corpus

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space (2012, methodology): “Originally, MrBayes only supported simple phylogenetic models, but the model space expanded considerably in version 3.0 (Ronquist and Huelsenbeck 2003).”
The human phylome (2007, methodology): “To obtain support values of all tree partitions, the ML tree produced by the best-fitting model was used as a seed for a Bayesian analysis by running Mr Bayes [21] for 100,000 gen-”
Phylogenetic classification of Trametes (Basidiomycota, Polyporales) based on a five–marker dataset (2011, methodology): “(iii) Bayesian analyses (BY) were run using MrBayes v.3.1 (Ronquist & Huelsenbeck, 2003) at the Cipres Science Gateway (Miller & al., 2010; http://www.phylo .org/) for 10 million generations, under a GTR model, with four chains, and trees sampled every 100 generations.”
Systematic relationships of hymenolepidid cestodes of rodents and shrews inferred from sequences of 28S ribosomal RNA (2010, methodology): “Phylogenetic analyses were based on the Bayesian approach (Huelsenbeck et al. 2001), performed using MRBAYES v. 3.1 (Ronquist & Huelsenbeck 2003).”
Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): higher classification and biogeography (2006, methodology): “BI Finally, we ran BI partitioned by codon position (first and second; third) in MrBayes 3.0b4 (Ronquist & Huelsenbeck, 2003), with the HKY85 + I + Γ model of sequence evolution for first and second positions, and GTR + I + Γ for third positions.”
Phylogeny and Biogeography of Tsuga (Pinaceae) Inferred from Nuclear Ribosomal Its and Chloroplast DNA Sequence Data (2008, methodology): “Bayesian analyses were conducted with MrBayes 3.1 (Ronquist and Huelsenbeck 2003) using default priors, four incrementally heated Markov chains, and two concurrent runs of 10,000,000 generations sampled every 50,000 generations for a total of 400 trees used to calculate posterior probabilities.”
Studies on woloszynskioid dinoflagellates IV: The genus Biecheleria gen. nov. (2009, methodology): “3.12, Ronquist & Huelsenbeck 2003) and maximum likelihood (ML) using PhyML (ver.”
A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes (2008, methodology): “1.1 (Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003), which carries out Metropolis-coupled Markov chain Monte Carlo sampling, was used to calculate Bayesian posterior probabilities.”
Genomic Organization, Differential Expression, and Interaction of SQUAMOSA Promoter-Binding-Like Transcription Factors and microRNA156 in Rice1[W] (2006, methodology): “Bayes phylogenetic trees were reconstructed with the programMrBayes version 3.0 (Ronquist and Huelsenbeck, 2003) under the JTT-f model of amino acid substitution and 4-g category model.”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, methodology): “Mixture trees, for example, are the result of supermatrix analyses in which alignments from multiple unlinked genomic regions are concatenated into a single matrix and analyzed using a model that assumes no recombination within the matrix (e.g., those employed in RAxML, MrBayes, etc.).”
Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies (2008, background): “1.2 (Ronquist & Huelsenbeck 2003) and included four independent runs with three heated chains and one cold chain in each run.”
Diplodia seriata, the anamorph of "Botryosphaeria" obtusa (2007, methodology): “Phylogenetic analyses of sequence data were done using PAUP* v.4.0b10 (Swofford, 2003) for Maximum-parsimony (MP) and Neighbourjoining (NJ) analyses and Mr Bayes v.3.0b4 (Ronquist and Huelsenbeck, 2003) for Bayesian analyses.”