BEAST Software - Bayesian Evolutionary Analysis Sampling Trees
BEAST is built on a large body of prior work and appropriate citations for individual modules, models and components will be listed when BEAST is run. BEAST-Users mailing list. Users are strongly advised to join the BEAST mailing-list. This will be used to announce new versions and advise users about bugs and problems.
First Tutorial | BEAST Documentation
An introductory tutorial to getting started with BEAST. This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate a phylogenetic tree. It will take you through the process of importing an alignment, making choices about the model, generating a BEAST XML file. You will then run BEAST.
Installing BEAST | BEAST Documentation
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.
Downloading and installing BEAST on UNIX/Linux
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).
Getting Started with BEAST | BEAST Documentation
You will then run BEAST. Second Tutorial This tutorial follows directly on from the first, looking at the output of BEAST, diagnosing problems and summarising the results. This tutorial will introduce some of the utilities packaged with BEAST, logcombiner and treeannotator, as well as the external applications, Tracer and FigTree.
Downloading and installing BEAST on Windows
Installing BEAST. Unzip the downloaded compressed ZIP archive (currently BEAST.v10.5.0-beta5.zip). The unzipped files contain executable binaries for BEAST, BEAUti, LogCombiner, TreeAnnotator and TreeStat. Double-clicking on those files will automatically start the corresponding program. BEAGLE acceleration library
FigTree | BEAST Documentation
FigTree is a program for viewing trees, including summary information produced by TreeAnnotator, and producing publication quality figures.
BEAGLE | BEAST Documentation
Using BEAGLE with BEAST 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 …
Phylogeographic diffusion in discrete space | BEAST Documentation
The first step will be to convert an alignment file in fasta format into a BEAST XML input file. This is done using the program BEAUti (this stands for Bayesian Evolutionary Analysis Utility). This is a user-friendly program for setting the evolutionary model and options for the MCMC analysis.
Estimating rates and dates from time-stamped sequences | BEAST ...
To inform BEAUti/BEAST about the sampling dates of the sequences, go to the Tips menu and select the “Use tip dates” option. By default all the taxa are assumed to have a date of zero (i.e. the sequences are assumed to be sampled at the same time; BEAST considers the present or most recent sampling time as time 0).