BEAUti
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BEAST Documentation->Programs->BEAUti
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Bayesian Evolutionary Analysis Utility (BEAUti).
BEAUti is a graphical user-interface (GUI) application for generating BEAST XML files.
- BEAUti ReadMe is included in BEAST ReadMe
- Version History
It is distributed in the same package as BEAST. To download it, go to the BEAST web page.
New in Version 1.5.x
BEAUti has been completely re-written to allow flexible handling of multi-partition analyses, including partitioning by substitution models, clock models and trees. BEAUti also supports the new *BEAST method.
New in Version 1.4.x
Multiple BEAUti windows and new File menu
Saving and loading Template Files
Instead of Saving and Opening BEAUti files which used to contain the sequence data along with any settings, BEAUti now saves and opens Template files which only contain settings. Thus, you can set up a particular model, save a template and then later when you load a different data set, open the template and apply those settings to the new data. The template will specify everything (including the options for Guess Dates if it was used prior to creating the template). The default names for the log files will still be taken from the stem of the NEXUS file imported.
Command-line BEAUti
The advantage of these template files is that they can be used in a non-interactive, command-line way which is useful for scripting or batch-processing of files. This is done by running BEAUti from a command-line, which will generally be called like this:
java -jar beauti.jar <nexus_file> <template_file> <beast_file>
Where <nexus_file>, <template_file> & <beast_file> are replaced by the name of the NEXUS file,
the template file and the BEAST file to be generated, respectively. For example:
java -jar beauti.jar primates.nex mytemplate.xml primates.xml
This will import the NEXUS file, apply the settings in the template file, generate the BEAST XML file and then quit without displaying any windows or dialog boxes.
Creating and using Taxon Sets
Tree log files when using relaxed clocks
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Alexei Drummond, Andrew Rambaut and Marc Suchard
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