I haven't been closing following this thread, so I'm not sure that this is relevant - but phytools has a function called 'force.ultrametric' (I believe) that does precisely what its name suggests it might.

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de BiologĂ­a
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/

On 5/3/2018 3:34 PM, David Bapst wrote:
Hmm. I hope that isn't the case - branching.times() is used pretty
widely in ape-dependent packages for getting node ages from dated
ultrametric trees, and if such minimally non-ultrametric trees can
cause branching.times throw negative node ages, then I'm really
concerned what impact that might have elsewhere in the R-phylo
universe.
-Dave

On Wed, May 2, 2018 at 2:30 PM, Brian O'Meara <bome...@utk.edu> wrote:
On Wed, May 2, 2018 at 2:53 PM, David Bapst <dwba...@tamu.edu> wrote:

Given that your tree appears to be non-ultrametric enough to cause
branching.times to throw some nonsensical node ages, if it is supposed
to be ultrametric. I recommend checking it carefully to figure out why
the tips seem to not quite be at the same distance from the root.


  Sometimes this happens with tree import from a file -- it could be a newick
tree with branch lengths precise to the hundredths but a lot of the R
ultrametric tests by default use higher precision (1e-08, iirc).

Best,
Brian





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