BEAST 2

Last updated
Bayesian evolutionary analysis by sampling trees
Stable release
2.7.4 / 2023-03-20
Repository https://github.com/CompEvol/beast2
Written inJava
Operating system Windows, Mac OS X, Linux
Type Phylogenetics software
License GNU Lesser General Public License
Website http://www.beast2.org/

BEAST 2 is a cross-platform program for Bayesian analysis of molecular sequences. [1] Using MCMC, 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 BEAST program [2] (which is still actively developed and has recently been renamed BEASTX) [3] . A notable feature of BEAST 2 is the packaging system which has simplified the process of implementing novel models.

Contents

Taming the BEAST is a community driven resource which teaches the use of BEAST 2 and related phylogenetic software. [4]

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 easier 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. [5]

LinguaPhylo

A related project is LinguaPhylo (LPhy). [6] LPhy is a probabilistic programming language for defining phylogenetic analyses with a syntax similar to OpenBUGS. It 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.

MASTER/remaster

A particularly important package in the BEAST 2 ecosystems is remaster [7] (formerly MASTER [8] ). Remaster is a tool for simulating population trajectories and phylogenies from birth-death and coalescent models. It is used in simulation studies to validate novel methodologies.

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. ↑ "BEAST Documentation".
  4. ↑ 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.
  5. ↑ "Comprehensive BEAST Archive Network".
  6. ↑ 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. Bibcode:2023PLSCB..19E1226D. doi: 10.1371/journal.pcbi.1011226 . PMC   10381047 . PMID   37463154.
  7. ↑ Vaughan, Timothy G. (2024). "ReMASTER: improved phylodynamic simulation for BEAST 2.7". Bioinformatics. 40 (1): btae015. doi:10.1093/bioinformatics/btae015. hdl: 20.500.11850/655887 . PMC   10796175 . PMID   38195927.
  8. ↑ Vaughan, Timothy G.; Drummond, Alexei J. (2013). "A Stochastic Simulator of Birth–Death Master Equations with Application to Phylodynamics". Molecular Biology and Evolution. 30 (6): 1480–1493. doi:10.1093/molbev/mst057. PMC   3649681 . PMID   23505043.
Science-symbol-2.svg

This scientific software article is a stub. You can help Wikipedia by expanding it.

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.