PHYLIP Consense tree not most parsimonious?

Gert-Jan Caspers gertjan at sci.kun.nl
Fri Feb 3 06:09:45 EST 1995

Hi phylogeny constructors,

In constructing molecular phylogenies using the PHYLIP package,
I encountered something which puzzles me.
I wanted a maximum parsimony tree with bootstrap values from my 
protein data set, so I ran the programs Seqboot, Protpars and
Consense, using the output from the earlier as input for the
However, when I ran the resulting tree and some other trees I
made up myself through Protpars again, using the User Tree option,
I found that one of my own trees was one step shorter than the
consense, bootstrapped, tree.
Is there a rationale for this? Isn't Seqboot-Protpars-Consense
the way to find the most parsimonious tree, with bootstrap values

Greetings from Nijmegen, surrounded by soaked dikes.
Gert-Jan Caspers	Dept. of Biochemistry
			University of Nijmegen
gertjan at sci.kun.nl	P.O.Box 9101		Phone +31 80 614255
			6500 HB Nijmegen
			THE NETHERLANDS		Fax   +31 80 540525

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