Bayesian evolutionary analysis by sampling trees
Stable release
2.7.4 / 2023-03-20
Repositoryhttps://github.com/CompEvol/beast2
Written inJava
Operating systemWindows, Mac OS X, Linux
TypePhylogenetics software
LicenseGNU Lesser General Public License
Websitehttp://www.beast2.org/

BEAST 2 is a cross-platform program for Bayesian analysis of molecular sequences.[1] It estimates rooted, timed phylogenies using a range of substitution and clock models, and a variety of tree priors. There is an associated tool, called BEAUTi, for setting up standard analyses (which are specified using XML). BEAST 2 is a complete re-write of the earlier (still actively developed) BEAST program[2] and as such draws on a large body of work. A notable feature of BEAST 2 is the packaging system which has simplified the process of implementing novel models.

Taming the BEAST is a community driven resource which teaches the use of BEAST 2 and related phylogenetic software.[3]

BEAUti

BEAUti stands for "Bayesian Evolutionary Analysis Utility." It is a graphical user interface (GUI) that is used to create the input files for BEAST 2. It allows users to easily specify the various options and settings for their phylogenetic analysis, such as the data file, the model of molecular evolution, and the prior distributions of model parameters. BEAUti also allows users to specify the parameters for the MCMC analysis, such as the chain length and the sampling frequency. This makes it a user-friendly way to run BEAST 2, as it eliminates the need for users to manually edit XML input files.

BEAUti allows users to easily install and manage different packages, such as models of molecular evolution or coalescent models. These packages can be installed directly from within BEAUti. This makes it easy to add new functionality to the analysis without needing to manually download and install the packages.

CBAN

The Comprehensive BEAST Archive Network (CBAN) is the official repository for BEAST 2 packages. Packages in CBAN can be installed via BEAUti out of the box.[4]

LinguaPhylo

A related project is LinguaPhylo (LPhy).[5] LPhy is a probabilistic programming language for defining phylogenetic analyses with a syntax similar to OpenBUGS. It is provides a way to generate BEAST 2 XML files (and similar model specifications for other phylogenetics packages) without needing to write the XML by hand.

References

  1. ↑ Bouckaert, Remoco (2019-04-08). "BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis". PLOS Computational Biology. 15 (4): e1006650. Bibcode:2019PLSCB..15E6650B. doi:10.1371/journal.pcbi.1006650. PMC 6472827. PMID 30958812. S2CID 104294209.
  2. ↑ Suchard, Marc (2018-06-08). "Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10". Virus Evolution. 4 (1): vey016. doi:10.1093/ve/vey016. PMC 6007674. PMID 29942656.
  3. ↑ Barido-Sottani, Joëlle (January 2018). "Taming the BEAST—A Community Teaching Material Resource for BEAST 2". Systematic Biology. 67 (1): 170–174. doi:10.1093/sysbio/syx060. PMC 5925777. PMID 28673048.
  4. ↑ "Comprehensive BEAST Archive Network".
  5. ↑ Drummond, Alexei J.; Chen, Kylie; Mendes, Fábio K.; Xie, Dong (2023). "LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses". PLOS Computational Biology. 19 (7): e1011226. doi:10.1371/journal.pcbi.1011226. PMC 10381047. PMID 37463154.
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