Dear colleagues,
I am trying to estimate ancestral states for two binary characters in a
full morphology-based phylogenetic tree. I am using ace function,
type="discrete" and kappa=0 as arguments. Unfortunately, I am dealing with
two problems about this issue: my topology have three polytomies and tree
branches have no lengths.
To perform ancestral state estimation, I firstly used the multi2di
function. However, this procedure creates artificial nodes in the topology.
This becomes a new problem, since states at these new nodes are also being
estimated.
Is there another way to deal with this situation? There are functions (or
packages) other than those of phytools that are able to deal with
polytomies and the absence of branch lengths in ancestral state
reconstruction?
Thanks in advance!
Diego
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