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Pileup Dendrogram (v8 vs.v9)

Jerry Learn learn at u.washington.edu
Mon Mar 23 11:52:23 EST 1998


I agree with other posters' comments on the use and misuse of guide
trees.  By no means should it be used as a phylogenetic tree. 

Although PAUP is included in the current version of GCG, I don't find it
easy to use and it's behavior seems to be unreliable (I can't remember
details). Until the standalone version of PAUP* becomes available later
this year (along with very rich documentation and online help), I
recommend either the old workhorse PHYLIP package (available from
<http://evolution.genetics.washington.edu/
phylip.html> or <ftp://evolution.genetics.washington.edu/pub/phylip>) or
the GCG programs distances and growtree if you don't need a maximum
likelihood or parsimony analysis.  While clustalw and clustalx are useful,
the phylogenetic analyses do not implement corrections for multiple
substitutions other than Kimura 2PD. Furthermore, to visualize and plot
the dendrograms you will need the PHYLIP package (or other tree drawing
programs e.g., treetool for SunOS, or TreeView for mac or PCs
<http://taxonomy.zoology.gla.ac.uk/rod/treeview.html>).

Good Luck!

Jerry Learn

Research Associate

Health Sci. Ctr., Rm. K443-C      |
Dept. of Microbiology             | Learn at u.washington.edu
University of Washington          | Phone: (206) 616-4286
Box 357740                        |   FAX: (206) 616-1575     
Seattle, WA  98195-7740  USA      |   


In article <E0yH3Rb-0003UD-00 at mail1.uct.ac.za>, ed at molbiol.uct.ac.za wrote:

> > 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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