IUBio

Pileup Dendrogram (v8 vs.v9)

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Mon Mar 23 03:33:21 EST 1998


In article <1998Mar20.140916 at bphvax>,
	caal at bphvax.biophysics.rochester.edu (Charles A. Alexander) writes:
> One of the users I support has a problem with Pileup V9's dendrogram plot.  He
> claims that the dendrogram plot in Version 8 is much more accurate.  After
> looking at the output from both those versions and consulting the manual, I
> have to agree.
> 
> Whatever the "method" was to draw Pileup V8's dendrogram, It seems the branch
> lengths correspond better to the distances between the sequences and are
> more proportional.  Anybody know why this is so?  I run GCG v9.1 on VAX/VMS 6.2

	Well, it doen't matter. As far as I know, PileUp does not use
the distances from the Guide Tree to weight sequences, so, only 
the order is used to drive the alignment. If the orders of the nodes
are the same, I think PileUp will work as usual.

	Anyway, this tree can not be used as a phylogenetic tree, 
I can't recommand using this tree for something else than
checking PileUp alignment order. Just have a look at PAUP
instead.

	Well, in the other hand, according to the recent tests we 
made with PileUp (while developping Clustal), I have to mention that... 
GCG completly screwed up PileUp in version 9.

					Sorry,
						François.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France



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