Help with Phylip

Joe Felsenstein joe at evolution.genetics.washington.edu
Mon Mar 9 19:57:18 EST 1998


In article <6e1sea$pp1 at net.bio.net>,
Tom Fagan  <bombadil at biosun.harvard.edu> wrote:
> ...  The trouble is that the output from consense doesn,t
>give any branch lengths and when I draw the tree with TreeView although
>the scale bar appears it is obviously meaningless.  Now the output from
>neighbor does have distances but 100  of them, it seems that in making a
>consensus tree this data does not get carried over, yet I have seen
>publications where the same applications were used and the nice little
>scale bar appears on the tree.  How is this scale calculated? Am I doing
>something wrong, - anyone got any ideas,

Yes.  The branch lengths on the consensus tree are the numbers of
replicates that support that branch.  This is not meaningless but
certainly not what you want.

I suggest you use the consensus tree as a User Tree (option U) in
a distance matrix program such as Fitch, and ask it, on the original
set of distances from the full data set, to infer branch lengths.
Then those can be plotted as in TreeView.

This and other such questions are answered in the PHYLIP web site
Frequently Asked Questions page:

http://evolution.genetics.washington.edu/phylip/faq.html

-- 
Joe Felsenstein         joe at genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA




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