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PHYLIP Consense tree not most parsimonious?

Joe Felsenstein joe at evolution.genetics.washington.edu
Fri Feb 3 20:00:50 EST 1995

In article <D3F8CA.Izz at sci.kun.nl> gertjan at sci.kun.nl (Gert-Jan Caspers) writes:
>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

No, it won't always find the most parsimonious tree.  For that you just
do a parsimony run on the full data.

The groups that have high support in the bootstrap will almost always
also show up in the most parsimonious tree as well -- the differences
between the two trees should be in the ill-supported region.  

Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet:         joe at genetics.washington.edu     (IP No.

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