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
latter.
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
included?
Greetings from Nijmegen, surrounded by soaked dikes.
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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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