Bootstrapping in PHYLIP vs PAUP

Derek Sikes dss95002 at UCONNVM.UCONN.EDU
Tue Oct 5 09:39:20 CDT 1999

Dear Taxacomers,

A coauthor and I have been analysing a dataset, he using PHYLIP, I using
PAUP 4.0b2.  Our bootstrap runs produce very different results:

Only two branches over 50% ( 70-90%) are found with PHYLIP repeatedly,
whereas PAUP finds only one branch over 50% (51%) and this branch is
neither of the two found by PHYLIP.  These are parsimony searches
(PHYLIP: DNA parsimony algorithm, version 3.572c).

I was wondering if anyone knew any particulars about why PHYLIP and PAUP
would produce such different bootstrap results?

secondarily I was curious if anyone knew about why PHYLIP generates a
bootstrap tree (using majority rule & strict consensus) with branches
supported less than 50%- PAUP collapses these and I would think that if
they are uncollapsed they must be randomly chosen from a shortest tree
topology ..


Derek Sikes

Derek Sikes
Dept. of Ecology and Evol. Biology U-43
University of Connecticut
Storrs, CT 06269  USA

FAX: 860-486-6364

dss95002 at

"Remember that Truth alone is the matter you are in Search after; and if
you have been mistaken, let no Vanity reduce you to persist in your
mistake." Henry Baker, London, 1785

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