BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Tree log -- file name

Tree log – 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.

See also trace file name.

Bayesian evolutionary analysis by sampling trees

Disclaimer: The above is the opinion of the author RB. If you do not agree, or spot a mistake, contact the author, or discuss this in the issues area or raise a new issue. A link will be added from this page to make sure others can find it.

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