BEAST protocols

BEAST specifications

Information


Unique identifier OMICS_04233
Name BEAST
Alternative name Bayesian Evolutionary Analysis by Sampling Trees
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.4.1
Stability Stable
Maintained Yes

Subtools


  • Tracer
  • TreeAnnotator

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Documentation


Publications for Bayesian Evolutionary Analysis by Sampling Trees

BEAST IN pipelines

 (108)
2018
PMCID: 5790234
PMID: 29381722
DOI: 10.1371/journal.pntd.0006190

[…] tracer [49] was used to visualize the results of the mcmc run. treeannotator [46] was used to summarize the information from the sample of trees produced onto a single target tree calculated by beast, with the first 2,500 trees being discarded as burn-in. figtree (http://tree.bio.ed.ac.uk/software/figtree/) was used to visualize the maximum clade credibility (mcc) tree., the vcf files […]

2018
PMCID: 5831051
PMID: 29489860
DOI: 10.1371/journal.pone.0192565

[…] the subsequent phylogenetic molecular clock analyses., virus population demographics and time to the most recent common ancestor (tmrca) were estimated using the relaxed-clock models implemented in beast version 1.8.4 [57] within a bayesian statistical framework. best partition scheme for the substitution models of the sequence alignment was selected using the bayesian information criterion […]

2018
PMCID: 5849722
PMID: 29535295
DOI: 10.1038/s41426-018-0028-y

[…] pcr purification kit (qiagen, barcelona, spain) and bi-directionally sequenced (macrogen inc., amsterdam, the netherlands). the phylogenetic analysis (bayesian analysis) was conducted using the beast package62, with the tn93 evolution model, a gamma distribution and invariable sites. the clock parameters were set to uncorrelated lognormal, using a coalescent constant size model. the chain […]

2018
PMCID: 5882731
PMID: 29657807
DOI: 10.1098/rsos.172141

[…] the muscle plugin [17] (with translation alignment of coding sequences) in geneious pro v. 10.0.2 [18] and checked by eye., time-calibrated phylogenies were estimated using bayesian inference in beast v. 2.4.7 [19]. a best-fit partitioning scheme and substitution models were determined for all possible codon positions for coding genes and all gene partitions using partitionfinder2 [20]. […]

2017
PMCID: 5224923
PMID: 28072390
DOI: 10.7554/eLife.20983.043

[…] was hky+i+γ using the program jmodeltest2 (darriba et al., 2012) and the built-in akaike information criterion (akaike, 1974). a bayesian maximum clade credibility tree was calculated using beast v1.8 (drummond et al., 2012) (rrid:scr_010228) and treeannotator (drummond et al., 2007) with the nucleotide data partitioned between coding and non-coding and a strict molecular clock […]

BEAST institution(s)
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland; Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand; Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK; Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
BEAST funding source(s)
A Rutherford Discovery Fellowship from the Royal Society of New Zealand; Marsden grant UOA0809 from the Royal Society of New Zealand; National Institutes of Health grant R01 HG006139; National Science Foundation grants DMS-0856099 and DMS-1264153

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