The "strange" shape of your tree seems to result from negative branch lengths.

If your goal is to just obtain an ultrametric tree under no specific assumptions, use

compute.brtime (yourtree, method="coalescent", force.positive=TRUE).

Where 'yourtree' must be an object of class phylo.  force.positive=TRUE will prevent negative branch lengths to occur in your tree.

I hope this helps.

Juan A. Balbuena


Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia                                  
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