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Pileup Dendrogram (v8 vs.v9)

Ed Rybicki ed at MOLBIOL.UCT.AC.ZA
Mon Mar 23 05:27:45 EST 1998


> Subject:       Re: Pileup Dendrogram (v8 vs.v9)

> 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
...
> 
> 	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.

Have to agree: the "tree" you get out of PileUp - however pretty - is 
only as much of a tree as the dendrogram Clustal uses to guide its 
subsequent alignment; in other words, it is a preliminary dendrogram, 
based on pairwise sequence alignements prior to the generation of the 
aligned matrix of sequences.  Which we throw away...!

Although I would not look at PAUP, given that we have ClustalW and 
X!!

                     Ed Rybicki, PhD  
      Dept Microbiology     |   ed at molbiol.uct.ac.za   
   University of Cape Town  | rybicki at uctvms.uct.ac.za
   Private Bag, Rondebosch  |  phone: x27-21-650-3265
      7700, South Africa    |   fax: x27-21-689 7573
    WWW URL: http://www.uct.ac.za/microbiology/ed.html      
                                        
"Every year is getting shorter, never seem to find the time..."



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