ANNOUNCEMENT : TREECON 3.0 for comfortable phylogeny !

Mark Siddall mes at zoo.toronto.edu
Sat Jun 4 00:08:21 EST 1994

In article <schwarze-030694194428 at fennel.bio.caltech.edu> schwarze at starbase1.caltech.edu (Erich Schwarz) writes:
>   I was thinking of situations where there is in fact one single most
>parsimonious tree.  As I understand the debate, one either can consider
>that tree to have a probability of effectively 100% (which I think is the
>cladistics position) or try to assign it some other probability (which I
>understand to be Dr. Felsenstein's position.)
>   Of course I may have gotten it wrong -- in fact cladistics may assign a
>less-than-100% value to the probability of the most parsimonious tree, or
>to the sum of probabilities of the equally most parsimonious trees...
>   Or the entire debate may be about something else altogether.  <sigh>
>--Erich Schwarz

This is likely no longer the correct forum for this so I'll be 
mercifully short...
Cladists do not assign probabilities to their most parsimonious tree(s)
except that they contend that by being most parsimonious, they are more
likely than those that are less parsimonious.  
The most ardent of us would suggest that ALL equally parsimonious tree
are equally well supported.
We start getting into grey area here when one considers the criterion of
choice by cladists to be more like goodness of fit, and, unless I am 
mistaken, the criterion of maxlik (Felsenstein) to be based more on
confidence than g-o-f.

I have yet to hear a compelling argument for something with a worse fit
to the data having a better p-value than something with a better fit but
then I don't claim to fully (or perhaps even partially) understand
maximum liklihood.

That wasn't at all short.. sorry.  Wanna move this to sci.bio.evolution 
or bionet.molbio.evolution???  Or maybe just drop it?


Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062

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