IUBio

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.

	Yep.

> 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 :

http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/help2.html



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 
	http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/help7.html

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.
	Remember YOU MUST ALIGN THE SEQUENCES FIRST!!!! 
	
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.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France




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