Hi Santiago,
it is possible to extract the information for the root for the sankoff
algorithm in the phangorn package (this is for discrete characters).
I'll added a function called pace, which will do the job. Of course
maximum parsimony will not provide unique solutions, but several
characters
Hi Timothee,
Assuming that I figured out your tree format correctly, I have written
you a function to translate your tree-as-data-frame into an object of
class phylo in R. I attach the disclaimer that this is programmed
very inelegantly and may contain errors. It also contains no method for
