Good point that I should have specified -- these are rooted trees I'm
working with. I've been using Molphy but I'm still reading up on how to get
it to calculate likelihoods for all 3 (rooted) cases.
I've wondered if there has been any literature comparison of any distance
methods versus ML specifically for a rooted, 3 taxa case? It seems that
rather than comparing likelihood values that comparing branch lengths and SE
measurements from NJ trees, for example, would be just as useful in
determining relationships between three taxa. Any thoughts on this?
"John Harshman" <harshman.diespamdie at sjm.infi.net> wrote in message
news:9qpurn$o8i$1 at mercury.hgmp.mrc.ac.uk...
> 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?
>> *Note the obvious spam-defeating modification
> to my address if you reply by email.