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