In article <9qpgtd$9fb$1 at mercury.hgmp.mrc.ac.uk>, iotarho
<iotarhorho at hotmail.com> wrote:
> 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.
I can offer you very little help. But I do have a question: why is the
minimum of 4 taxa a problem? With 3 taxa there is only one tree, so there
can be no comparison of likelihoods among topologies. If you have a
program that works fine except for requiring 4 taxa, go with it.
And have you tried MOLPHY?
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