how to OUTGROUP IN BEAST

[Oshin Ley Garcia]

Hi everyone, I included an outgroup sequence in my alignment and tried to create a taxon set for it in BEAUti, but the model failed with XML errors.

Is there a correct way to define an outgroup inside BEAST, or should I only root the tree after the analysis is finished?

Thanks

[Alexei Drummond]

Hi Oshin,

You should definitely not re-root the tree after a BEAST analysis. BEAST produces a sample of rooted trees based on the chosen time-tree model and any manipulation afterwards would violate the assumptions of the analysis.

If you have an outgroup I presume you want to put a monophyletic constraint on the ingroup? That is possible, but you just need to make sure that your starting tree obeys that constraint if you have a starting tree.

Cheers

Alexei

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