BEAST 2

BEAST 2 is a bioinformatics software package for Bayesian evolutionary analyses of molecular sequences, reconstructing phylogenies, and testing evolutionary hypotheses. The BEAST 2 algorithm uses Markov chain Monte Carlo (MCMC). A variety of additional user-installable tools/packages is available.

Topic

Phylogenetics;Phylogenomics

Detail

  • Operation: Phylogenetic tree reconstruction;Phylogenetic tree analysis (shape)

  • Software interface: Command-line user interface;Graphical user interface

  • Language: Java

  • License: GNU Lesser General Public License v 2.1

  • Cost: Free

  • Version name: 2.6.7

  • Credit: Rutherford Discovery Fellowship (http://www.royalsociety.org.nz/programmes/funds/rutherford-discovery/) from the Royal Society of New Zealand, Marsden grant from the Royal Society of New Zealand (http://www.royalsociety.org.nz/programmes/funds/marsden/awards/award-2008-2/), National Institutes of Health (http://www.nih.gov), National Science Foundation (http://www.nsf.gov).

  • Input: -

  • Output: -

  • Contact: Remco Bouckaert r.bouckaert@auckland.ac.nz, Alexei J. Drummond alexei@cs.auckland.ac.nz

  • Collection: BEAST

  • Maturity: Mature

Publications

  • Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
  • Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002 Jul;161(3):1307-20. doi: 10.1093/genetics/161.3.1307. PMID: 12136032; PMCID: PMC1462188.
  • https://doi.org/10.1093/genetics/161.3.1307
  • PMID: 12136032
  • PMC: PMC1462188
  • Bayesian coalescent inference of past population dynamics from molecular sequences
  • Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005 May;22(5):1185-92. doi: 10.1093/molbev/msi103. Epub 2005 Feb 9. PMID: 15703244.
  • https://doi.org/10.1093/molbev/msi103
  • PMID: 15703244
  • PMC: -
  • Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics
  • Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 2008 Jul;25(7):1459-71. doi: 10.1093/molbev/msn090. Epub 2008 Apr 11. PMID: 18408232; PMCID: PMC3302198.
  • https://doi.org/10.1093/molbev/msn090
  • PMID: 18408232
  • PMC: PMC3302198
  • Phylogeography takes a relaxed random walk in continuous space and time
  • Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol. 2010 Aug;27(8):1877-85. doi: 10.1093/molbev/msq067. Epub 2010 Mar 4. PMID: 20203288; PMCID: PMC2915639.
  • https://doi.org/10.1093/molbev/msq067
  • PMID: 20203288
  • PMC: PMC2915639
  • BEAST: Bayesian evolutionary analysis by sampling trees
  • Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007 Nov 8;7:214. doi: 10.1186/1471-2148-7-214. PMID: 17996036; PMCID: PMC2247476.
  • https://doi.org/10.1186/1471-2148-7-214
  • PMID: 17996036
  • PMC: PMC2247476
  • Bayesian random local clocks, or one rate to rule them all
  • Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all. BMC Biol. 2010 Aug 31;8:114. doi: 10.1186/1741-7007-8-114. PMID: 20807414; PMCID: PMC2949620.
  • https://doi.org/10.1186/1741-7007-8-114
  • PMID: 20807414
  • PMC: PMC2949620
  • Bayesian phylogeography finds its roots
  • Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots. PLoS Comput Biol. 2009 Sep;5(9):e1000520. doi: 10.1371/journal.pcbi.1000520. Epub 2009 Sep 25. PMID: 19779555; PMCID: PMC2740835.
  • https://doi.org/10.1371/journal.pcbi.1000520
  • PMID: 19779555
  • PMC: PMC2740835
  • BEAST 2: a software platform for Bayesian evolutionary analysis.
  • Bouckaert R, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. BEAST 2: a software platform for Bayesian evolutionary analysis. 2014; 10:e1003537. doi: 10.1371/journal.pcbi.1003537
  • https://doi.org/10.1371/journal.pcbi.1003537
  • PMID: 24722319
  • PMC: PMC3985171
  • BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
  • Bouckaert R, Vaughan TG, Barido-Sottani J, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650. PMID: 30958812; PMCID: PMC6472827.
  • https://doi.org/10.1371/journal.pcbi.1006650
  • PMID: 30958812
  • PMC: PMC6472827

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