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Protocols

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 No

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Publications for MrBayes

MrBayes citations

 (6281)
call_split

Genetic diversity of PRRSV 1 in Central Eastern Europe in 1994–2014: origin and evolution of the virus in the region

2018
Sci Rep
PMCID: 5958080
PMID: 29773820
DOI: 10.1038/s41598-018-26036-w
call_split See protocol

[…] yzed in the study (Supplementary Table). Sequence alignment was performed based on ClustalW (Geneious 10.1.3, Biomatters) and phylogenetic analysis using a Bayesian Markov chain Monte Carlo method in MrBayes v3.2. Detailed parameter settings and the principles of lineage definitions were identical to those described previously. A general time-reversible nucleotide substitution model with 4 categor […]

library_books

An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

2018
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 were […]

call_split

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] were realigned using Geneious and trimmed at the N terminus to the first methionine present and at the C terminus to the last residue of the protein (with 70% identity). Trees were inferred using the MrBayes and RAxML programs inbuilt into the CIPRES webserver (table S1). A Bayesian tree was inferred using three substitution models (GTR, Jones, and WAG), a minimum of 600,000 generations, and an in […]

library_books

High species diversity of trichostrongyle parasite communities within and between Western Canadian commercial and conservation bison herds revealed by nemabiome metabarcoding

2018
PMCID: 5952520
PMID: 29764472
DOI: 10.1186/s13071-018-2880-y

[…] ned, 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. […]

library_books

Microscopic and Molecular Evidence of the First Elasmobranch Adomavirus, the Cause of Skin Disease in a Giant Guitarfish, Rhynchobatus djiddensis

2018
MBio
PMCID: 5954223
PMID: 29764943
DOI: 10.1128/mBio.00185-18

[…] nloaded 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. […]

library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] hs and (ii) use the corrected Akaike information criterion (AICc) for model selection. ML and BI analyses were performed using the RAxML web-server (http://embnet.vital-it.ch/raxml-bb/index.php ) and MrBayes v3.2.4 under the best substitution models and partition scheme identified (Supplementary Table ). Bayesian analyses were run with the settings nst = 6 and rates = invgamma for the ND and aamod […]


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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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