phylip verses paup

Joe Felsenstein joe at evolution.genetics.washington.edu
Fri Dec 22 14:25:43 EST 2000

In article <9206aa$qi0$1 at mercury.hgmp.mrc.ac.uk>,
rob dean  <tabco at arches.uga.edu> wrote:
>his may not be the right thread for this question but I will throw it
>out anyway.  In consense when two sequences are exactly the same why do
>you not get 100/100 for the bootstrap values?  I have looked a all 100
>trees individually and in each case you get the straight line indicating
>complete similarity but when you use consense you get a number ranging
>from 94-96.  Any thoughts?

I'm not sure why you said "two sequences are exactly the same", perhaps you
meant "two trees are exactly the same".  In such a case you should get
100 percent for the bootstrap values.  Therefore if you are right that all
the trees are the same, there is a bug.  To check this, send me the input
file of trees (not as an Attachment but as the body of an email message.

I will double check and let people know what I find.

Joe Felsenstein         joe at genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA


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