Dear all,
I want to get squared change parsimony ancestral state reconstructions for
a matrix into R.
I have tried the asr_max_parsimony() function from castor, but the results
are not the same as in Mesquite for example. To take an example, a
two-taxon clade with a unique state for these taxa optimized as having a
different state (shared by near relatives) at the ancestral node. This
doesn't happen in Mesquite and is *not* what I want.
If there were some way to get the results from Mesquite into R that would
also be OK, but I cannot figure out the node numbering system in Mesquite,
to match them up with nodes as numbered by ape.
Any help would be *very* greatly appreciated.
Best wishes,
Roland
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