Hello all,
I recently decided to manually edit a very large supertree (1700
taxa) in Mesquite (I had to collapse a few nodes into polytomies,
something I can only seem to do in Mesquite). I read it out of R as a
Newick file, than into Mesquite, where I did my little edits and then
saved the tree
In my lab we've been messing with the new phylobase package, which has a
different nexus reader than ape. The package will create a different tree
object, but I think there is also a converter in there to get to ape format.
Might be worth a try.
To collapse nodes you could use the function di2multi() in ape which
collapses all internodes with a length below tol (specified by the
user). If your tree doesn't have branch lengths, you could just set all
the edge lengths of the edges you want to keep to 1, and all the other
ones to 0, and
Hi David,
there are a few superfluous brackets in your tree (161) and (185)
around single tips. If you remove them read.tree works fine. These
also explains un-collapsed double node branches, you produced them
with adding the brackets.
Cheers,
Klaus
PS: There is a function collapse.singles in
