generating an ultrametric tree from a non-ultrametric tree?

[Alison Ravenscraft]

Hi DPPDIV users,

I have a non-ultrametric tree that was generated in RaxML.  I want to convert the tree to an ultrametric tree.  I've heard that I should use DPPdiv. but I'm not sure how.  What would the command line look like for this?  (I do have a copy of the alignment file from which the tree was generated.)

I'm mostly confused because I don't have any calibrations to enter. I don't need to know the absolute divergence times, I just need an ultrametric tree that has reasonable relative branch lengths.

Thank you in advance!  Sorry if my question is unclear; I am very new to this type of analysis.

Best,
Alison

[Tracy Heath]

Hi Alison,

Sorry for the slow response. You can estimate relative branch times in DPPDiv and most other programs (e.g., RevBayes, BEAST). For all of the Bayesian programs, you have to choose a relaxed clock model and tree prior. In DPPDiv, if you don't provide any calibrations, the times and rates estimated are all relative, with the root age fixed at 1.0. 

Cheers,

Tracy

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