Bootstrap and Happiness

newsmgr at newsmgr at
Mon Dec 22 13:32:20 EST 1997

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Subject: Re: Bootstrap and  Happiness
Message-ID: <19971222163601.LAA15490 at>
From: foxik at (Foxik)
Date: 22 Dec 1997 16:36:40 GMT
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Thank you, Dr. Felsenstein, I will use 1000 replicates as a standard option=

I have some other questions to you if I may ask.

Zharkikh and Li (1992) in their paper stated: <<As long as reasonable numbe=
r of
bootstrap replicates (say, >=3D 100) have been conducted, considerable (=3D=
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 supporte=
d by
<=3D75% of the replicates...>>=20

Both PHYLIP and GCG-PAUP are using bootstrap 50% majority-rule consensus tr=
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 betwe=
50-75% if the segregation is most likely to be erroneous?

The other question is: If there is any difference in bootstrap trees produc=
by PHYLIP and PAUP. I mean if the following PHYLIP message which doesn=92t =
on PAUP trees is applicable to the later (keeping in mind that PAUP is show=
percent not an absolute numbers):
<<the numbers at the forks indicate the number of times the group consistin=
g of
the species which are to the right of that fork occurred among the trees, o=
of 1000.00 trees>>.=20

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