I'm looking for an ML program to do, for protein sequences, an exhaustive
search of tree space and report the log likelihood score for each possible
tree. Of course I'll only be using this for small #'s of taxa (3-6), but I
haven't been able to get this result with the more commonly used PC software
without a significant amount of user input (e.g. having to input each user
tree to be scored). So far I've tried Phylip, PAML, and the Vanilla package
and each one seems to have a dead end drawback, either that there's no PC
executable, the software doesn't do protein ML, a minimum of 4 taxa are
necessary, etc.
Is there a program out there that will do this or is there a workaround I'm
missing for one of the mentioned programs?
Thanks in advance.
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