BEAST protocols

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BEAST specifications


Unique identifier OMICS_04233
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


  • Tracer
  • TreeAnnotator



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Publications for Bayesian Evolutionary Analysis by Sampling Trees

BEAST in pipelines

PMCID: 5789282
PMID: 29403651
DOI: 10.1093/ve/vex044

[…] samples as burn-in, setting posterior probability limit to 0.1 and reconstructing node height based on common ancestor heights criterium. the mcc trees were visualised using figtree v1.4.0 (). the beast 2 source files and analysis scripts can be found in the file., first, we set out to estimate the start of the epidemic and the clock rate of the zikv epidemic for (1) the complete data set […]

PMCID: 5790234
PMID: 29381722
DOI: 10.1371/journal.pntd.0006190

[…] correlation between genetic divergence and time for the m. leprae strains (). therefore, the data were found to be suitable for molecular clock analysis., the snp alignment was analyzed using beast v1.8.4 []. the calibrated radiocarbon dates of the ancient strains in years before present (ybp, with present being considered as 2017), the isolation years of the modern strains, […]

PMCID: 5790234
PMID: 29381722
DOI: 10.1371/journal.pntd.0006190

[…] burn-in. tracer [] was used to visualize the results of the mcmc run. treeannotator [] 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 ( was used to visualize the maximum clade credibility (mcc) tree., the vcf files […]

PMCID: 5802765
PMID: 29410410
DOI: 10.1038/s41598-018-20187-6

[…] (s) were estimated using the dnasp v.5., we estimated the relative age of divergence between the two mitochondrial lineages using the bayesian relaxed phylogenetic approach implemented in beast v.1.8.4, based on the combined mitochondrial genes. the substitution model was determined using the software partitionfinder version 1.1.1. that selected the gtr + g + i model. a strict […]

PMCID: 5825158
PMID: 29432421
DOI: 10.1371/journal.pgen.1007155

[…] using splitstree v.4.12.3 [], with confidence values calculated with 1,000 bootstrap iterations. we built maximum clade credibility trees using the bayesian phylogenetic tools implemented in beast v.1.8 [] (see below)., transforming the variant sites into a fasta format, we estimated genetic diversity as watterson´s θ [] and nucleotide diversity π, and the difference between these two […]

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BEAST in publications

PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] with 199 derived alleles (16% of the total snvs) unique to this y-chromosome., to infer the tmrca of y-chromosome clades, we used the bayesian markov chain monte carlo approach implemented in beast, which yielded the same tree topology as obtained with raxml (fig. ). we calibrated our estimates by setting a prior tmrca at the root of the phylogeny as 1.5 million years ago (mya) based […]

PMCID: 5944922
PMID: 29746563
DOI: 10.1371/journal.ppat.1006997

[…] in ., using the radiocarbon dates for the ancient samples and the isolation dates for the modern samples as tip calibration points we estimated the divergence time for all m. leprae strains using beast [] assuming a constant population size [] and a variable population size by application of a bayesian skyline model []. the age of the most recent common ancestor (mrca) was estimated to 4,515 […]

PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] using path-o-gen v1.4 (ſtware/patho- gen/) with the ml tree for non-recombinant genomic sequences (alignment available from: we used beast program v1.82 (), with the estimated evolutionary rate prior (m = 4.8e-4 ± 2e-4 substitution/site/year) under a relaxed lognormal molecular clock and a gtr+g+i substitution model to infer […]

PMCID: 5954268
PMID: 29764421
DOI: 10.1186/s12864-018-4461-z

[…] influenza virus sequence annotation tool provided by ncbi [], and then the cdss were aligned to codon positions using muscle []. then, the bayesian markov chain monte carlo (mcmc) implemented in beast v2.4.4 [] was used to infer a time-tree from the alignment. the beast software was run under the hky substitution model, a bayesian skyline coalescence model, and a strict molecular clock model […]

PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] sativus was obtained from genbank., chloroplast and 45snrdna sequences from 28 genotypes were subjected to tree topology analysis and divergence time estimation using bayesian methods implemented in beast ( the beast program assumes auto-correlation, and is widely used to estimate the uncertainty of divergence dates and branch lengths, to estimate divergence using […]

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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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