[BiO BB] Clustering
idoerg at burnham.org
Wed Sep 3 12:19:08 EDT 2003
Dan Bolser wrote:
> What packages support clustering of points
> with a with a similarity matrix?
I don't think I quite understand the question, can you elaborate on that?
> How can I derive the similarity of two matrices?
If you mean that you would like to check how "close" two similarity
matrices (e.g. BLOSUM, PAM) are to each other, then one method is to
compare the amino-acid pair frequency distributions used to construct
these matrices. Look to the following paper (fig 4, and the last
paragraph in the "methods" section) for one example on how to do this,
although other methods of comparing distributions may be used just as
Iddo Friedberg, Ph.D.
The Burnham Institute
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