FigTree won't export .nwk with posterior probabilities

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Mark Hanson

Feb 20, 2024, 12:13:30 PMFeb 20
to beast-users
Hi all, new to the group, and to BEAST in general. Running into a weird problem...

To confirm what I've done:
  • Ran BEAST 2x
  • Used logcombiner on both .log and .trees file to make one file, burnin applied
  • Used TreeAnnotator to combine trees
  • Opened mcc.tre file in FigTree, posterior probabilities are present in my mcc.tre file
  • Then when I save as .nwk, the posterior values aren't coming with and all that's included are the branch/node lengths/ages.

I must just be missing a box to tick or something... Anyone know what's going on?


My .tre file:
Example of my .nwk output:

Mark Hanson

Feb 20, 2024, 12:26:26 PMFeb 20
to beast-users
Apologies, in the meantime I've realized my core problem isn't related to file type. Newick doesn't retain metadata like this. I'm trying to use my tree in an MCMCglmm() but my values of phylogenetic heritability (vp/(vp+vs) keep coming up as ~0.5 independent of treatment. I thought this had to do with support values being brought through the analysis, but as the previous (functional) analysis used a .nwk tree, this can't be why. Indeed, the code I'm using works with a different .nwk tree. But when I input my tree and build my MCMCglmm models, it fails to yield realistic results...

Any experts in MCMCglmm that could offer advice, much appreciated.
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