BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Species tree logger -- file name

Species tree logger – file name

Name of the file, or stdout if left blank. File names can be parameterised, and there are a few build-in parameters:

• $(filebase) is replaced by the XML file name minus .xml • $(seed) is replaced by the random number seed

So, if you set the file name to $(filebase)-$(seed).trees and use a file beast.xml with seed 123 it saves the tree log in beast-123.trees.

You can also define your own parameters, and run BEAST with the -D option to define the parameter. For instance, setting the file name to $(filebase)-$(run).trees and running BEAST with

beast -D run=76 beast.xml


results in the tree file being written in beast-76.trees.