I wonder if you could do something with Monte Carlo simulation?--
either ask the question "How often will one tree produce sequences this
unrelated?" or "How often will multiple disjoint trees produce sequences
this related?" You will need a reasonably plausible model of sequence
evolution, which may not be easy to come by: but without one I'm not
sure *any* statistical test will do much for you.
Mary Kuhner mkkuhner at genetics.washington.edu
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