I have posted this question at Stack Overflow. I hope this doesn't violate
any community rules about double posting.
I probably could have worded the title better, but I am wanting to collapse
any clade within a phylogenetic tree (even if the clade has one member)
which has a tip label of "foo" and then count the number of tips which were
dropped from that specific clade and create a branch with a tip label
displaying 35 foos.
The counting portion is easy; however, when I use
drop.tip(rooted.tree,tip=which(rooted.tree$tip.label=='foo'),subtree=TRUE)
the dropped tips do not maintain their position in the tree. Rather, they
are all grouped at the end (counted properly however). Is there anyway to
collapse a clade by tip labels and maintain its position
BranchLizard
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