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.

Cheers

yan
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