Bootstrap and Happiness

Joe Felsenstein joe at evolution.genetics.washington.edu
Tue Dec 23 11:03:37 EST 1997

In article <67mbnk$jo5 at net.bio.net>,  <newsmgr at merrimack.edu> wrote:
>From: foxik at aol.com (Foxik)
>I have some other questions to you if I may ask.
>Zharkikh and Li (1992) in their paper stated: As long as reasonable number of
>bootstrap replicates (say, >= 100) have been conducted, considerable (>80%)
>confidence may be given to a tree  that is supported by >80% of replicates.
>On the other hand little confidence can be given to a tree that is supported
>by 75% of the replicates...
>Both PHYLIP and GCG-PAUP are using bootstrap 50% majority-rule consensus tree
>as a standard option. Why a standard cutoff is not 75%? In other words, why
>somebody would like to see cluster segregation occurring at the level between
>50-75% if the segregation is most likely to be erroneous?

Just for completeness.  You can always ignore them and collapse those parts
of the tree.  On the other hand they are suggestive.

>The other question is: If there is any difference in bootstrap trees produced
>by PHYLIP and PAUP. I mean if the following PHYLIP message which doesn't show
>on PAUP trees is applicable to the later (keeping in mind that PAUP is showing
>percent not an absolute numbers):
><<the numbers at the forks indicate the number of times the group consisting
>of the species which are to the right of that fork occurred among the trees,
>out of 1000.00 trees

Just because that message isn't printed out by PAUP I don't think there is
any difference between the trees.  In PHYLIP we do also add some groups
below 50% (I think PAUP does not).  But the rest of the tree should be the

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

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