BEAST
BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a package of programs for evolutionary inference of molecular sequences designed by Andrew Rambaut and Alexei Drummond (Drummond et al. 2002; 2005; 2006). It is orientated toward rooted, time-measured phylogenies inferred using molecular clock models. It can be used to reconstruct phylogenies and is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses Bayesian MCMC analysis to average over tree space, so that each tree is weighted proportional to its posterior probability.
Version 1.5b2
Input data file format
BEAST requires infiles to be in the XML format; however, BEAUti will convert NEXUS files into XML for you.
Instructions
First, format your NEXUS file using BEAUti, then run BEAST. To view and analyze your data use Tracer and TreeAnnotator. LogCombiner is a program to combine log and tree files from multiple runs of BEAST. All four programs can be downloaded from the BEAST web site. Use FigTree to view trees and divergence time estimates.
On a UNIX operating system, run the following commands:
BEAST is available at the BEAST web site and further information regarding the program can be found in the manual
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BEAUti (Bayesian Evolutionary Analysis Utility) is a graphical software program that allows the creation of XML input files for BEAST. There are five panels in BEAUti (Data, Model, Priors, Operators, and MCMC), each of which contain multiple parameters that can be configured. Prior information from fossils and other sources can be used to create the XML file. BEAUti can also create and open template files which only contain settings of a particular model. This template can be used later for a longer MCMC run, or for a different data set.
Version 1.5b2
Input data file format
Instructions
To run BEAUti from the command line, type:
Some configurations must be edited manually in the XML file that the program generates. For details on how to edit specific parameters in the XML file, refer to the program manual.
BEAUti is available for Macintosh, Windows, and Linux platforms, and can be download from the BEAST web site.
