> Another way to put it is that I would like to know if this
> collection of sequences is monophyletic on the grand tree of
> all gene trees, or if it is para/polyphyletic with the intervening
> sequences being of different function. While this is
> fundamentally a phylogenetic question (presuming such a
> grand tree of all gene trees exists), it is a horrendous one
> to answer in that the sequences are so divergent that
> one can't do a normal phylogenetic analysis on them - there's
> just nothing to get a hold of.
OK, I'll give it another try. If you want to test the monophyly of
the sequences, I can think of a potential likelihood ratio test, or
maybe Faiths T-PTP test might be appropriate. The likelihood ratio
test would work on the idea that you could constrain the search such
that the sequences of interest are monophyletic (or nonmonophyletic).
You could calculate the likelihood under this constraint (L0) and also
when this constraint is relaxed (L1). The distribution of the LR test
statistic could be determined through simulation under the null hypothesis.
Would this test what you want?
John
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John & Edna Huelsenbeck
johnh at mws4.biol.berkeley.eduednah at mws4.biol.berkeley.eduhttp://mw511.biol.berkeley.edu/john/edna.html
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