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
