phylip verses paup

Mary K.Kuhner mkkuhner at kingman.genetics.washington.edu
Sat Dec 23 12:32:26 EST 2000

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?

Is it possible that you have *three* sequences exactly the same?
In that case, the bootstrap trees (assuming you are using a
method that cannot create trifurcations) will resolve them 
arbitrarily, and the consensus program may not be clever enough
to recognize that two trees whose only topological difference
involves zero-length branches are really the same.

What programs are you using?  It's also possible you've found a

Mary Kuhner mkkuhner at genetics.washington.edu


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