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.
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.
CBANedit
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]
LinguaPhyloedit
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.
beast, cross, platform, program, bayesian, analysis, molecular, sequences, estimates, rooted, timed, phylogenies, using, range, substitution, clock, models, variety, tree, priors, there, associated, tool, called, beauti, setting, standard, analyses, which, spe. 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 Bayesian evolutionary analysis by sampling treesStable release2 7 4 2023 03 20Repositoryhttps github com CompEvol beast2Written inJavaOperating systemWindows Mac OS X LinuxTypePhylogenetics softwareLicenseGNU Lesser General Public LicenseWebsitehttp www beast2 org Taming the BEAST is a community driven resource which teaches the use of BEAST 2 and related phylogenetic software 3 Contents 1 BEAUti 2 CBAN 3 LinguaPhylo 4 References 5 External linksBEAUti editBEAUti 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 editThe 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 editA 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 edit 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 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 Barido Sottani Joelle 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 Comprehensive BEAST Archive Network Drummond Alexei J Chen Kylie Mendes Fabio 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 External links editOfficial website nbsp This scientific software article is a stub You can help Wikipedia by expanding it vte Retrieved from https en wikipedia org w index php title BEAST 2 amp oldid 1188017515, wikipedia, wiki, book, books, library,
