A long time ago (late 1970s), Walter Fitch and a postdoc (Ron ????) of his
had a program ANCSTR, written in Univac 1108 Fortran, which did this. I
assume it's been ported to more current machines. Try checking with him. I
hope this helps.
James McInerney wrote:
>> 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?