I am having a problem trying to unambiguously reconstruct ancestral
sequences. I know it is possible to resolve ancestral sequences _with_
ambiguity, but what about making some educated guesses and/or
assumptions and then deciding to construct unambiguous ancestral
sequences (sort-of like maximum likelihood). We can choose among
competing alternatives using a pre-constructed substitution matrix to
choose which ancestor might be the most likely. The problem we are
finding arises when we get to the root.
Is there any method that has been published that will succesfully
reconstruct ancestral sequences based on a tree, without having to
resort to introducing ambiguous residues?