MCC Tree of Discrete Phylogeographic Diffusion Model

[BruinsFan]

Hi,

I have a MCC tree of a discrete phylogeographic diffusion model. It is
a very large tree with 200 + taxa.
For some reason, states (locations) are missing from some of the
branches and internal nodes.
Is this because branches or nodes in the the MCC must have states with
a set that has a large enough posterior probability? Can this
threshold be adjusted in TreeAnnotator?

Thanks, Matthew

[Philippe Lemey]

Dear Matthew,
The missing states are probably due to the "Posterior probability limit" setting in TreeAnnotator, which has a default of 0.5. With this setting, all nodes with posterior probability < 0.5 will not be annotated. Simply set this to 0 to obtain all annotations -- this will be the default in the upcoming BEAST release.
Kind regards,
Philippe

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[Camilo Khatchikian]

Hi Matthew,

Yes, you need to change in TreeAnnotator the box "posterior probability limit" from the default value (0.5) to 0. That should do it. Good luck.

Best Regards,

Camilo Khatchikian

UPenn