Hi David and Leandro,
Thanks very much for the suggestions and the code.
I tried Leandro's approach of forcing PAUP to create binary trees - most
of my simulated datasets had a few extra trees but a small minority had
A LOT of trees (one had an extra 300 000) so now I see David's point
about
Hi David,
Thanks for the response. I did not consider the computational
difficulties primarily because my polytomies are small - usually only
involving 3 tips. I think your extract.clade() -- allTrees() --
bind.tree() suggestion would work well. This is actually for a
simulation study where
Alistair-
Even if all the polytomies are small, if there are many of them, the
number of potential trees may be very large. I don't know the exact
numbers.
The following, for a phylo object named tree should give you a
vector which identifies those nodes that are polytomies (have more
than 2
Good day all,
I was wondering if there was any way to get multi2di to return trees
with all possible combinations when breaking up a polytomy to a
dichotomous branching tree?
The reason why I ask is that PAUP is returning non-binary trees from
some analyses (e.g. a set of most parsimonious
Alistair-
How many multifurcations are there, with how many branches each? If
the number of potentially resulting trees is too high, it may not be
possible to store all the possible trees in memory.
If your tree is small, you might try allTrees(), which is the only
ready to use function I know
