Re: Bootstrap analysis question2.

[david peters <davidrpeters@earthlink.net>]

The matrix is 83% filled.

I'm actually wondering if there is a button in the Mac version of PAUP that 
enables one to estimate bootstrap values after a Heuristic search. I note that 
I am able to do so by taking the cladogram apart, branch by branch and only 
performing the bootstrap analysis on fewer than 10 taxa at a time.

But is this valid? Or not?

David Peters
St. Louis


-----Original Message-----
From: "Jaime A. Headden" <qilongia@yahoo.com>
Sent: May 20, 2005 1:57 PM
To: DML <dinosaur@usc.edu>
Cc: david peters <davidrpeters@earthlink.net>
Subject: Re: Bootstrap analysis question.

david peters (davidrpeters@earthlink.net) wrote:

<Can a bootstrap analysis be performed on it using PAUP?

And if so, what are the steps?>

  Bootstrapping is a PAUP feature, but is also found in a few other programs
such as Clustal, MEGA, etc., which are less used by the phylogenetics recovery
nerds. If it takes that long to boostrap, you have too many variables and
unknowns, and the likely result will be a complete collapse of all nodes in the
resulting tree. That is, a confidence of 0 in any node. This usually results
from a high proportion of "?".

  Cheers,

Jaime A. Headden

  Little steps are often the hardest to take.  We are too used to making leaps 
in the face of adversity, that a simple skip is so hard to do.  We should all 
learn to walk soft, walk small, see the world around us rather than zoom by it.

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)


                
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