[Biopython-dev] Bio.Cluster

Iddo Friedberg idoerg at burnham.org
Fri Jun 13 18:10:11 EDT 2003

Dear Michiel,

I just looked at the manual for Bio.Cluster (very well written, BTW). Is 
there a way to do a k-means clustering (or other) based on a distance 
matrix, rather than on the gene expression vector data? The data i am 
trying to cluster teh structural similarity of protein structure 
fragments, and as such already appears in the matrix form.



Michiel Jan Laurens de Hoon wrote:
> Dear biopython developers,
> I have added Bio.Cluster to the Biopython CVS. Bio.Cluster contains 
> clustering techniques for gene expression data (hierarchical, k-means, 
> and SOMs); most routines are written in C with a Python wrapper. This 
> package also exists separately as Pycluster.
> The Python and C source code is in Bio/Cluster; I have also added 
> Bio.Cluster to setup.py.
> In case you want to try this package, there is a manual at
> http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/cluster.pdf
> (replace "from Pycluster import *" by "from Bio.Cluster import *") and a 
> sample data set at
> http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/demo.txt.
> Please let me know if you find any problems with this package.
> --Michiel.

Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

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