MrBayes pipeline

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

Subtool


  • BEST

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Fredrik Ronquist <>

Publications for MrBayes

MrBayes IN pipelines

 (216)
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 [62] were used for phylogenetic analysis. akaike information criteria (aic) test in jmodeltest v.2.1.7 [63] was used to evaluate the likelihood parameters set for bi analysis. […]

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

[…] substitution models (using 3 substitution schemes) were compared with jmodeltest 265 and best-fit models selected based on the akaike information criterion. bayesian analyses were performed using mrbayes 366. 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: 5811015
PMID: 29438445
DOI: 10.1371/journal.pone.0192723

[…] using the iqtree multicore v.1.5.3 with jtt + g4 model [22]. branch supports were assessed by bootstrapping with 1,000 standard replicates. bayesian inference of phylogeny was conducted using mrbayes 3.2.6 with analysis run for 1 million generations, sampling every 100th of them [23]. the model of site heterogeneity was set based on iqtree analyses (g4), while the optimal model of amino […]

2018
PMCID: 5811015
PMID: 29438445
DOI: 10.1371/journal.pone.0192723

[…] generations, sampling every 100th of them [23]. the model of site heterogeneity was set based on iqtree analyses (g4), while the optimal model of amino acid substitutions (jones) was found by mrbayes using mixed amino acid model prior., leishmania mexicana (isolate mnyc/bz/62/m379) culture was maintained in m199 medium (sigma-aldrich, st. louis, usa) supplemented with 2 μg/ml biopterin […]

2018
PMCID: 5814415
PMID: 29449610
DOI: 10.1038/s41598-018-21400-2

[…] in the genbank database of ncbi (http://www.ncbi.nlm.nih.gov/) and mycobank (http://www.mycobank.org/), and aligned using clustal_x v.1.8139. bayesian inference of the phylogeny was performed in mrbayes version 3.2.140, with permutations allowed until a frequency of division ≤0.01 was reached. the general time-reversible (gtr) substitution model was used. figtree version 1.4.241 was used […]

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].

MrBayes reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MrBayes