[Biodevelopers] Any simple clustering program for Hierarchical Single Linkage available?

[Dan Bolser]

Shalini Sridhar wrote:
> Hello All,
> 
> I need a simple , freely downloadable , Clustering program , that will 
> cluster a large number of records (>10,000) using Hierarchical 
> Clustering Methods, and using Single Linkage Clustering Technique.
> 
> I would like to cluster a large number of proteins based on a similarity 
> score that will be used as input and to output a tree in the form of a 
> text file.
> 
> This program needs to be run from command line, prefereably a C 
> executable from a UNIX machine. The input would be a text file of a 
> distance matrix and the output will also be a text file of clusters or 
> dendrograms.
> 
> I came across OC - Geoffery Barton - University of Dundee, that fits my 
> required description, however the output is just a PS file, and thus 
> cannot be manipulated further.
> 
> I also came across Eisen Lab's - CLuster3.0 , however, this is more 
> complicated and used for mostly microarray data, since the input and 
> output file fits the requirement for microarray sets.
> 
> Could someone please suggest me a simple program that would fit my 
> description required? Would really appreciate it.
> 

I found the statistical analysis software R exelent for basic clustering.

Not sure if it will scale to a 10,000 x 10,000 size matrix, but on a 
machine with lots of memory it may do fine.




> Thank you.
> 
> Shalini Sridhar
> 
> MRes.Bioinformatics and Computational Biology, Univ of Leeds,Leeds.
> 
> 
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