BEAST pipeline

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 citations

 (36)
2018
PMCID: 5933809

[…] site duplication (tagctgat), consistent with integration mediated by the flanking is26 transposases of tn6029., we constructed a dated phylogeny of all available s. typhi 4.3.1 from nepal, using beast2 (fig 6, interactive version available at https://microreact.org/project/rjnfyogxg). this analysis yielded a local substitution rate of 0.8 snps per genome per year (95% highest posterior […]

2018
PMCID: 5904502

[…] was selected through the akaike information criterion (aic) with the software jmodeltest2 (darriba et al. 2012). the xml input files were generated with beauti 1.8.0, and the bi was performed with beast 1.8.0 (drummond et al. 2012). a yule speciation process, with a random starting tree, and relaxed molecular clock was used as tree priors. four markov chain monte carlo (mcmc) searches […]

2018
PMCID: 5862453

[…] best fit in the sequence alignment; wag with site heterogeneity model gamma plus invariant sites (g+i). the bayesian analyses were carried out using markov chain monte carlo (mcmc) implemented in beast 1.7.5 package [95]. we ran four independent mcmc searches using distinct randomly generated starting trees. each run consisted of 50-million generations, and trees were sampled every 1,000 […]

2017
PMCID: 5773327

[…] at 95% for each node., we used the bayesian binary mcmc (bbm) method implemented in rasp 3.0.0 to estimate the possible ancestral areas of triplostegia with the trees obtained from the intraspecific beast analysis (yu, harris, blair, & he, 2015). three geographical regions that represent the current distribution of triplostegia were defined: southwestern china (sw; east himalayas […]

2017
PMCID: 5604429

[…] viruses. the respective nucleotide alignment was translated to protein level in the p and s-corresponding reading frames and bayesian trees were reconstructed for both protein sequences using beast (drummond et al., 2012) with the substitution model selected by prottest (abascal et al., 2005) and a yules speciation prior. lengths of the branches (measured as amino acid substitutions per […]

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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