Sorry if this is a trivial question, but I have some (rooted) nexus trees with
polytomies at the root. When I read them in using read.nexus() they are treated
as unrooted. What’s the easiest way to tell R that they are intended to be
rooted, even though the root is a polytomy? There’s no ‘force.rooted’ option to
any of the tree reading routines that I can see.
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