bootstrap values

Byron J. Adams bjadams at CRCVMS.UNL.EDU
Mon Feb 12 13:49:48 EST 1996

>Could someone help me?
>I work on 14 sequences (rDNA of the ITS region) of Lipomyces strains. I
>have make an alignment of my sequences using pileup program of GCG. After
>that, I have use the .msf file for analysing the file with the package
>I have made 1000 bootstaps using SEQBOOT and then calculate the most
>parsimonious tree with DNAPARS. But, when I look to the tree, I don't see
>the bootstraps value. How can I see on the postscript tree file the
>bootstrap values.
>What is the best way to analyse the data and to find the tree?
>DNA parsimonious <-> DNA branch and bound algorythm <-> Maximum likelihood
>analyses <-> ... ?
>Charles Moulliard (moulliard at mbla.ucl.ac.be)

        In response to your question about viewing treefiles, I have found
the program TreeView to be particularly helpful.  It will display the
treefiles you create using the executables you mention in PHYLIP.  It will
operate from a Macintosh or Windows platform and can be got from:


        As for how to evaluate, align, and use your sequences to recover
evolutionary history (and then evaluate this hypothesis), I can only
suggest that you really dig into these subjects thoroughly, exploring the
more philosophically and operationally satisfying alternatives.  References
for some of the seminal papers along these lines can be found in the main
documentation that accompanies the PHYLIP package, and this would be a good
place to start.
        Even though I work on the ITS region myself, I can only suggest
that you familiarize yourself with your data set, then go about exploring
some of the many tree building options that are available.  Get to know
what these programs do, how they do it, and particularly what assumptions
they make concerning the treatment of your characters.  As is often the
case, interesting questions rarely have simple answers, and in this case
the best answer to the question, "which way is best?" is, "It depends..."

Byron J. Adams                      Keep Utah Wilderness Wild!
University of Nebraska              Ask your Senator to
406 Plant Sciences Hall             Oppose S-884
P.O. Box 830722
Lincoln, NE 68583-0722              "Wilderness, once we have given
(402) 472-2858                       it up, is beyond our
fax (402) 472-2853                   reconstruction."
bjadams at crcvms.unl.edu                     -Wallace Stegner
badams at unlgrad1.unl.edu

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