Probabilities on Phylogenetic Trees

Richard Zander bryo at COMMTECH.NET
Thu Sep 11 07:40:13 CDT 1997


Stuart G. Poss wrote:

>a colleage who may have a different, if not
> entirely clear view of what he means.

Yes, but what I mean clears for me as the discussion continues, which is
what feedback is for, and I'm grateful for it. Simply put, I'd like a
measure of when my shortest tree has more evidence for than against. I
think there is a mathematical measure, though not exactly sure what it
is.
  Also, if my shortest tree isn't well-supported, I'd like to identify
portions of the cladogram that have more evidence for than against. (I
think this is what people mean by "we don't think our cladograms are
necessarily exactly right, but they are probably mostly right." Surely
one can provide a measure of how right various subclades are other than
the open ended ones of Bremer support, etc.)
  I think that if you have poor support (evaluated as the probablility
of being the true tree is < .5), then you have a cluster of terminal
taxa that theoretically is better than phenetic clustering. If you have
better than .5 probability throughout or in a subclade, then you have,
finally, a probabilistic hypothesis, which can be refined further by
testing the regularity assumptions and the model.
  That's more clear. Who can help with this?

--

*******************************************************
Richard H. Zander, Buffalo Museum of Science
1020 Humboldt Pkwy, Buffalo, NY 14211 USA bryo at commtech.net
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