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Pileup Dendrogram (v8 vs.v9)

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Tue Mar 24 03:20:33 EST 1998

In article <1998Mar23.124136 at bphvax>,
	caal at bphvax.biophysics.rochester.edu (Charles A. Alexander) writes:
> Thanks to all who responded to my question.  I never recommend Pileup's
> dendrogram for evolutionary relationship but in this particular case, it's
> what the user wanted and the length of the branches (perhaps coincidentally)
> seem to correspond to the respective percent identity.

	It should, but percent id is not enough to make
phylogenetics... Like others said, you should take more
information into account to evaluate the "real" evolutionary
distance between your proteins.

	%id is not the good information, weight of each mutation
and multiple substitutions IS the information you should try to
find while making a phylogenetic analysis.

	The Guide tree compute distances derived from a pairwise alignment,
phylogenetic analysis should be based on a (hopefully good) multiple
alignment. Please give to your user some introduction papers from
Joe Felsenstein, tis should help.

> I'm very grateful to you for taking the time to answer and also to Eric Cabot
> at GCG who clarified what the problem was (ie. scoring matrices).  
> If there's interest, I'll post his reply here.

	Well, I think that scoring matrices is a recurrent subject
in the GCG community... At Heidelberg, we discuss about alf an hour about
GCG scoring matrices, but teresult in GCG9 is not what we attempted.
(ouch! I think I'm losing my english today...).

						Best of luck,

P.S.: I just realized that the %id should not change if you use 
accurate matirces and algorithm, so branch lengths should not be
different between v8 and v9 of PileUp... That is probably what your
user asked first!
	But, if in the original publication, describing this method,
the %id is used (which is still the case for Clustal), GCG Pileup
uses a similarity score to build the tree, so changing the matrices will
change the branch lengths (see Progam Manual). So using such tree
as a phylogenetic base will drop you to a chicken and egg problem...
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France

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