MrBayes specifications

Information


Unique identifier OMICS_04237
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.2.7
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Fredrik Ronquist <>

MrBayes articles

MrBayes citations

 (77)
2018
PMCID: 5940881

[…] of invariant sites, as selected by jmodeltest v.255., to analyze the phylogenies of the 84 asian lineage strains, including the novel indian sequence, a bayesian phylogenetic tree was computed using mrbayes v.3.2.656 with the dataset including the 5 african zikv lineage strains as an out-group. two parallel runs with four metropolis-coupled chains were initiated for 5 m markov chain monte carlo […]

2018
PMCID: 5923257

[…] amino acid sequences were aligned using clustalw in geneious 7.1.7 (biomatters ltd, auckland, new zealand) and manually trimmed to 1268 positions. the consensus protein tree was inferred using mrbayes v3.2.6. amino acid substitution rates were modeled using the blosum matrix, γ-distributed rate variation across sites and a proportion of sites being invariable. markov chain monte carlo […]

2018
PMCID: 5851622

[…] of alignment unaligned or packed columns in msa were removed manually using jalview[36] software retaining good quality columns. phylogenetic trees were built based on bayesian inference using mrbayes software version 3.2[37] using mixed amino acid model. markov chain monte carlo (mcmc) analysis is utilized to approximate posterior probabilities of phylogenetic trees. an analysis […]

2018
PMCID: 5821076

[…] primarily amplified ntm were combined to improve primer specificity. the nondegenerate forward and reverse primer stocks comprised six forward and four reverse primers, respectively (see text s2)., mrbayes version 3.2 (60) was used to create a bayesian inference phylogenetic tree with alignment performed with clustalw. specifically, the 942- to 957-bp amplicons were fitted to a general […]

2018
PMCID: 5817148

[…] all loci. the alignments were estimated using mafft version 7 (http://mafft.cbrc.jp/alignment/server/; katoh & standley, 2013)., phylogenetic trees were reconstructed from alignments using mrbayes v.3.2 (ronquist et al., 2012), selecting a general time reversible substitution model with a proportion of invariable sites and a gamma‐shaped distribution of substitution rates across sites […]

MrBayes institution(s)
Department of Biodiversity Informatics, Swedish Museum of Natural History, Stockholm, Sweden; Department of Scientific Computing, Florida State University, FL, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Genome Center, University of California, Davis, CA, USA; Department of Mathematics, Stockholm University, Stockholm, Sweden; Departments of Statistics and Botany, University of Wisconsin, Madison, WI, USA; Departments of Agriculture and Natural Resources, Delaware State University, Dover, DE, USA; Departments of Biomathematics, Biostatistics and Human Genetics, University of California, Los Angeles, CA, USA; Department of Integrative Biology, University of California, Berkeley, CA, USA
MrBayes funding source(s)
Supported by the Swedish Research Council [2008-5629]; the National Institutes of Health [GM-069801 and GM-086887, HG-006139], the National Science Foundation [DEB-0445453, DEB-0949121, DEB-0936214, and DBI-0755048].

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