Bootstrap trees and PAUP

Joe Felsenstein joe at
Sun May 23 12:51:44 EST 1999

In article <7i2a9r$3v6 at>,
Mark Dowton  <Mark_Dowton at> wrote:
>... One problem with this is that if some replicates
>generate many equally parsimonious trees (say 100), while others only
>generate a single (or a few) most parsimonious tree(s), the maj. rule tree
>will be overly influenced by those replicates in which many equally
>parsimonious trees are found.
>I was under the impression that this was also a problem (although
>admittedly minor in most cases) with the bootstrap tree, but a friend
>tells me that the PAUP bootstrap tree corrects this.  Is this the case?

I am virtually certain that PAUP corrects for this (I know that PHYLIP
does too).  One counts the trees when there are 100 of them as 0.01 of
a tree each, in doing the consensus tree.

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

More information about the Mol-evol mailing list