BEAST 2: keeping topology constant while estimating other parameters

[Michael Forthman]

Hello,

I believe I have formatted the xml file correctly to input a starting tree. However, I would like divergence times to be estimated on this topology, and thus need to keep the topology constant. The BEAST 2 wiki page states that I should remove the Tree operators from the xml file, or give them zero weight. The wiki gives a list of operators to tackle: narrow exchange, wide exchange, Wilson Balding, subtree slide.

I had a couple questions regarding this information. First, are these the only tree operators I need to find in the xml file or do others (e.g., tree scaler, tree root scaler) need to be edited too? Should I remove the command lines or is it preferred to set the weights to zero?

Thanks for any assistance, Michael

[Remco Bouckaert]

Hi Michael,

The tree operators mentioned on the wiki are operators that change the topology of the tree. The tree scaler, tree root scaler and uniform operator are operators that leave the topology of the tree unchanged, but do change the heights of the nodes in the tree (there may also be up-down operators that scale the tree at the same time as scaling some other parameters). So, if you would like to fix the topology and estimate divergence times, you should leave these last set of operators in the XML, but disable the topology changing operators.

Cheers,

Remco

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[Michael Forthman]

Hello Remco,

Thank you very much for the clarification. Do you know if it matters whether I element the string of text that is associated with these particular operators, or just put a value of "0" in "weight="?

Cheers, Michael

[Remco Bouckaert]

Setting the weight=“0” ensures the operator is never chosen during the BEAST run. You mean ‘delete’ not ‘element’, right? Deleting (or commenting out by wrapping it inside <!— and —>) the operator from the XML has the same effect as setting the weight to zero.

Cheers, Remco