I have a set of rooted trees, some of which have polytomies at the root, like
These are not treated as rooted by default, so I have tried to root them using
root(tree, node = Ntip(phy) + 1, resolve.root = TRUE), but this gives an error,
Note that in my case there is no particular reason to specify either A, B, or
(C,D) as an outgroup
I should explain that what I am trying to do is to calculate distance metrics
between these trees (using metrics that are valid with polytomies, such as the
KC metric), such that the pairwise distances between (A,B,(C,D)) and
(B,A,(C,D)) and ((C,D), B, A) etc are all 0, but the distance between, say,
(A,B,(C,D)) and ((A,B),(C,D)) or perhaps (A,C,(B,D)); is not zero.
So how can I specify a polytomy at the root, with the tree format used in R?
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