I’m looking for a method that would enable me to predict with some confidence value the most likely trait for a tip on my phylogeny. For example, I have a set of sequences from different locations except that the location for one of the sequences is missing. I would like to predict this missing trait and get a probability for the assignment. I thought that something like the ancestral character evolution (ace in APE) might work but it only seems to allow for known traits at the tips.
I’m currently making the assumption that my phylogeny is correct but if it was possible to apply a method that allowed for uncertainty in the phylogeny by providing a sample of trees from a bayesian phylogenetic reconstruction, that would be very useful.
Any suggestions or guidance would be very much appreciated.