While auteur will complain if given a polytomous tree, one can randomly
resolve the polytomies (using the multi2di function in ape, for
instance). The BM likelihoods of the data given any of the randomly
resolved trees will be identical. Be warned that if the polytomies are
soft, this will simply be a way to get auteur to 'work' -- rate
estimates will be low balled in the unresolved clades.
Jon
On 9/20/12 3:00 AM, r-sig-phylo-requ...@r-project.org wrote:
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Dear List,
taking advantage of the discussion, I'd like to ask if I could do these
test of rate heterogeneity in brownie.lite or auteur with a polytomous
tree. Apparantly, auteur only accepts a fully dichotomous tree. Is there
any alternative?
Thank you in advance,
Diogo
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