PHYLIP versus PAUP?

newsmgr at merrimack.edu newsmgr at merrimack.edu
Thu Dec 4 10:29:35 EST 1997


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Newsgroups: bionet.molbio.evolution
Subject: Re: PHYLIP versus PAUP?
Message-ID: <19971204140800.JAA18453 at ladder02.news.aol.com>
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Date: 4 Dec 1997 14:08:36 GMT
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Dr. Felsenstein,
I greatly appreciate your reply to my post. It is a big advantage of this
newsgroup when you questions could be answered by the author of the PHYLIP
himself.=20

<<I think that if the one doesn't make send but the other does, then you ne=
edto
understand unrooted trees and what they mean. >>

Yes, this is exactly the case. I don=92t understand the value of unrooted t=
rees.
I will try to illustrate my point in a separate post with a specific exampl=
e.
Meanwhile I would like to clarify for myself some other issues related to
PHYLIP and PAUP.

1. Do I understand correctly that the weblike tree produced by the DRAWTREE=
 of
the PHYLIP is a unique feature of this package and is not available in othe=
r
packages including PAUP*? Actually an unrooted tree produced by DRAWTREE is
very meaningful tree for me. On the other hand, a tree produced from the sa=
me
input file  by DRAWGRAM looks very different for me. For the DRAWGRAM to gi=
ve
me a tree topology which I can interpret the same way as in the DRAWTREE tr=
ee I
have to root it at the midpoint.

2. For the bootstrap analysis what is the bootstrap cutoff value for=20
statistically significant and not significant clustering? I saw some author=
s
are using 70%. Is it commonly accepted figure?  Exactly what level of
confidence 70% bootstrap value provides?

<<I'll let some experienced PAUP user answer your other question.  I am sur=
e
PAUP (and PAUP*) do have bootstrap values available.>>

I have received a private e-mail from the GCG help desk (help at gcg.com)
explaining how I can find bootstrap percentages produced by the PAUP*.  In =
the
past I contacted them directly on several occasions and received very valua=
ble
help. I didn=92t realize that PAUP is now fully supported by the GCG.




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