Probabilities on Phylogenetic Trees

Tom DiBenedetto tdib at UMICH.EDU
Sun Sep 14 19:00:35 CDT 1997


On Thu, 11 Sep 1997 07:40:13 -0700, Richard Zander wrote:

>Simply put, I'd like a
>measure of when my shortest tree has more evidence for than against.

I dont understand. Given that there are a finite number of trees, the
"evidence
against" must refer to evidence for an alternative. The shortest tree
has more
evidence supporting it than does any of the alternatives, By
defintion. If you
want to know whether your shortest tree has more evidence supporting
it than
there is evidence for all alternatives combined, then I wonder,,,why?
What is
the significance, or even the meaning of that?

>  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.

once again, why would the branch be present in the shortest tree if
there wasnt more evidence for it than against it?

> (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.)

What is your problem with Bremer support, and why do you need an
alternative?

>  I think that if you have poor support (evaluated as the probablility
>of being the true tree is < .5),

Sorry I havent been following the thread carefully (been out of the
country), but how can such a thing be calculated without knowledge of
the true tree? Are you basing
that on some belief that a particular model is an accurate mirror of
evolutionary process?




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