newsmgr at merrimack.edu newsmgr at merrimack.edu
Wed Dec 3 03:54:58 EST 1997

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Subject: PHYLIP versus PAUP?
Message-ID: <19971202213101.QAA24748 at ladder01.news.aol.com>
From: foxik at aol.com (Foxik)
Date: 2 Dec 1997 21:31:53 GMT
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I have several questions about PHYLIP and PAUP:

1. If the PHYLIP  SEQBOOT-DNAPARS-CONSENSE is run an <<outfile.>> contains
bootstrap values. If the PAUP (integrated to GCG 9.1) Paupsearch(brep=3D100=
branch and bound, parsimony) is run how one can find bootstrap values for
phylogenetic grouping? Or, a more general question: Is PAUP providing any
statistical support for the phylogenetic clusters it is producing?
2. If I draw(gram) a Consense tree from PHYLIP it doesn=92t have any sense.
However, if I have used SEQBOOT-DNADIST-NEIGHBOR and than rearranged a neig=
<<treefile.>> with the Retree (midpoint rooting) the resulting tree has a l=
of sense. The question is if I can transfer bootstrap values from a consens=
tree (SEQBOOT-DNADIST NEIGHBOR-CONSENSE) to a retreeted neighbor tree?

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