Dr. Nate Samuels
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BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without ...
Installing BEAST. BEAST has been developed in Java, which allows the same code to run on any platform that has the Java software installed. We have also created packages for each of the common operating systems to provide a user-interface that is ‘native’ and familiar.
BEAST can be downloaded from the following link: BEAST X v10.5.0-beta5 - UNIX/Linux version 46.2MB; This will download a compressed tar archive (a ‘.tgz’ file).
Jun 17, 2016 · Download BEAST v1.8.4 binaries for Mac, Windows and UNIX/Linux. Version 1.8.4 released 17th June 2016. New Features: New structured list of citations printed to screen before running. Option ('-citation_file') to write citation list to file. Option in BEAUti Priors panel to set parameters to 'Fixed Value'.
First cmd-select all kappa parameters, and select ‘Link parameters into a hierarchical model’. In the new Phylogenetic Hierarchical Model Setup window, enter a Unique Name (e.g. kappa), set the Normal Hyperprior Stdev to 5.0 and the Gamma Hyperprior Shape and Scale to 0.01 and 100.0 respectively and click OK: This operation can be repeated ...
Jul 9, 2024 · BEAST X is the new name for BEAST v1 project and the first release version of this is v10.5.0 which supersedes v1.10.4 in the old version system. From now on we will use the full major, minor, bugfix style of semantic versioning. Thus, this version is not BEAST 10 but BEAST X v10.5 (the 10th major, 5th minor release of the original BEAST project).
BEAUti is a graphical user-interface (GUI) application for generating BEAST XML files. It is distributed in the same package as BEAST. To download it, go to the BEAST download page. Run BEAUti by double-clicking on the BEAUti icon in the package you downloaded. See here for a guide to using BEAUti to create BEAST input XML.
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can make use of highly-parallel processors such as those in graphics processing units (GPUs) found in many PCs. The current version of BEAGLE will only work with BEAST v1.6 or later.
To help you get started with BEAST and get familiar with the different components and the work-flow we have put together a series of introductory tutorials that you can work through. First Tutorial. An introductory tutorial about running BEAST. Second Tutorial. An introductory tutorial about interpreting BEAST output. Estimating Rates and Dates.
To ensure that BEAST keeps the supplied tree fixed and does not sample from the posterior of trees, go to the Operators tab and select fixed tree in the Operator mix dropdown menu. Generating the XML and Analysing the Data. See the Analysing Continuous Traits tutorial for
