MrBayes protocols

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MrBayes specifications

Information


Unique identifier OMICS_04237
Name MrBayes
Software type Framework/Library
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 <>

Publications for MrBayes

MrBayes in pipelines

 (303)
2018
PMCID: 5751821
PMID: 29295716
DOI: 10.1186/s13071-017-2577-7

[…] submitted to the genbank database (ncbi) and assigned specific accession numbers (mf496203 and mf496204; mf693831–mf693833)., bayesian inference (bi) and monte carlo markov chain (mcmc) analysis in mrbayes v.3.2.3 [] were used for phylogenetic analysis. akaike information criteria (aic) test in jmodeltest v.2.1.7 [] was used to evaluate the likelihood parameters set for bi analysis. posterior […]

2018
PMCID: 5769553
PMID: 29335015
DOI: 10.1186/s13071-018-2615-0

[…] database under the accession numbers kt724974–kt725197., dna sequences were aligned with clustalx [] and phylogenetic trees were constructed for each gene under the bayesian inference method using mrbayes v.3.2.5 [, ]. the best-fit substitution models f81 + g (clock gene) and sym + g (cpr gene) were selected following the bic criterion as implemented in jmodeltest []. indel information […]

2018
PMCID: 5773594
PMID: 29348650
DOI: 10.1038/s41598-018-19620-7

[…] substitution models (using 3 substitution schemes) were compared with jmodeltest 2 and best-fit models selected based on the akaike information criterion. bayesian analyses were performed using mrbayes 3. two parallel metropolis-coupled markov chain monte carlo searches, each with four chains (3 ‘heated’), were run for 2 × 106 generations, sampling trees and parameters every 100 […]

2018
PMCID: 5804287
PMID: 29440965
DOI: 10.3897/phytokeys.95.21832

[…] implemented in mega v 7.0.25 () and subsequently adjusted manually., bayesian inference (bi) of phylogeny was performed on the concatenated data set of three genes (rbcl, matk and its) using mrbayes v. 3.2 (, ). the hierarchical likelihood ratio test (hlrt) and akaike information criterion (aic) were used to select the best model of evolution using mrmodeltest v. 2.3 (). the nucleotide […]

2018
PMCID: 5804921
PMID: 29378020
DOI: 10.1093/gbe/evy011

[…] combined iterations (). after deletion of segments that did not align unambiguously, alignments were subjected to bayesian inference for phylogeny reconstruction using a mixed amino acid model in mrbayes software (). analyses were run until convergence, and trees were rooted at midpoint (). for the earliest diverging branches of each major clade, closest homologs were identified by blastp […]


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MrBayes in publications

 (4509)
PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] 22 c. psittaci strains described in this study and additional 22 previously described c. psittaci strains, we constructed a mid-point rooted bayesian phylogenetic tree. the tree was constructed with mrbayes with the gtr + i model, and run parameters including four markov chain monte carlo (mcmc) chains with a million generations, sampled every 1000 generations and with the first 10,000 trees […]

PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536

[…] across the tree of life. finally, we constructed a phylogeny of all isip1 sequences (fig. s8; see table s1 for alignments). the diatom sequences formed a robustly supported monophyletic clade (mrbayes posterior probability = 1; raxml bootstrap support > 95%, both under three substitution matrices), to the exclusion of the pelagophyte, haptophyte, and dinoflagellate sequences. however, […]

PMCID: 5952520
PMID: 29764472
DOI: 10.1186/s13071-018-2880-y

[…] and a consensus sequence generated using a 75% threshold., all consensus sequences were then aligned in geneious using muscle, with default parameters and a phylogenetic tree was computed with the mrbayes plugin with the gtr substitution model, with 500,000 chain length and rooted on the trichuris discolor consensus sequence., fecal egg/oocyst counts for strongyle, nematodirus, trichuris, […]

PMCID: 5954223
PMID: 29764943
DOI: 10.1128/mBio.00185-18

[…] from genbank. helicase protein sequences were aligned using mafft with the e-ins-i alignment strategy and previously described parameters (, ). bayesian inference trees were constructed using mrbayes, with every 50 generations of the markov chain, monte carlo (mcmc) chain sampled, for a maximum of 1 million generations. the first 25% of mcmc samples were discarded as burn-in., guitarfish […]

PMCID: 5958175
PMID: 29780270
DOI: 10.3897/mycokeys.25.23836

[…] using the programme raxml-hpc2 v.8.2.10 on xsede () and bootstrap values were estimated with 1000 pseudo-replicates. bayesian inference analysis and posterior probabilities were calculated using mrbayes v.3.2.1 () with the markov chain monte carlo (mcmc) algorithm. four chains and two independent runs were carried out with 10 million generations. every 100th tree was saved into a file […]


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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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