[BiO BB] Looking for a tool to do protein sequence clustering/ordering

lavi Birdie gopu_36 at yahoo.com
Fri Jan 20 19:44:59 EST 2006

  I am looking for a tool to do protein clustering. My aim is, 
given a set
   of protein sequences, I want an output which is sorted according to 
their distance from each other. Basically, clustering as 1 whole cluster 
(not  according to their families). The basic idea is by using pairwise 
alignment  between all the sequences, sequences with minimum distance will be 
assigned  first and then progressively aligning the sequences on either side 
depending  upon the distance in the pairwise alignment score. This is basically 
using  Taylor's method or some other hierarchical clustering strategy.  So for a given 
set of   input sequences, a matrix will be constructed initially with their 
pairwise  alignment scores and then constructing sequences from minimum 
distance and  adding the rest of the sequences progessively. If some one can 
suggest some  tool to perform this sequence ordering, it would be more timely help 
for me.
 Regards Lavi

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