ClustAl W for trees ?

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Wed Mar 31 02:56:21 EST 1999

In article <Pine.A41.4.05.9903310027500.281284-100000 at asterix.uni-muenster.de>,
	"Carsten Hohoff" <hohoff at uni-muenster.de> writes:
> I have aligned 80 protein sequences with ClustAlW & used the .dnd output
> file for display by TreeView. Now a colleague told me that this output file
> is NOT appropriate for generating phylogenetic trees.


> Is this statement correct ? 

	Of course it is.

> I checked a web manual for ClustAlW / X, but could not find a direct hint on
> this subject.

	Well, you did'nt check it properly. If you read :


Multiple alignments are carried out in 3 stages (automatically done from menu item 1 ...Do complete multiple alignments now): 

    1.all sequences are compared to each other (pairwise alignments); 
    2.a dendrogram (like a phylogenetic tree) is constructed, describing the
    approximate groupings of the sequences by similarity (stored in a file).   
    3.the final multiple alignment is carried out, using the dendrogram as
    a guide. 

	So, as you can see, the dendrogram is just an tree baseed on similarity
which depends of the matrix used and is based on a fast pairwise comparison.
This can't give any idea about the way proteins diverge, and the position
specific mutations porobability.

If you then check out the page 

Which title is "Phylogenetic trees", you will read :
	1) Before calculating a tree, you must have an ALIGNMENT in memory.
	This can be input in any format or you should have just carried out
	a full multiple alignment and the alignment is still in memory.
So clearly, a phylogenetic tree is based on an alignment.

Now, at the end of the same page, you will read :

	(Get the PHYLIP package anyway if you are
	interested in trees). 

Because clustal provides only ONE method for the phylogenetic tree calculation,
which could be inadapted to your case.

> Hoping that someone might give a helpful hint

Hoping that you don't feel this answer too rough, I advise you to read
at least  "A brief guide to phylogenetic software" (TIG 14(11): 473-475)
by doug Eernisse, which can help you in understanding who is doing what
in the field.

				Best regards,

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

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