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
>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?
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. 128.95.12.41)
