I am trying to estimate ancestral states for two binary characters in a full morphology-based phylogenetic tree. I am using ape::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 ape::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?