One of my favorites is the MEV micro-array data analysis tool. It is simple to use and it has a very large number of features.

Works well for any type of data. You can also load into it data from a file that is in a simple text format:

GENE1, value1, value2
GENE2, value1, value2

Feel free to post your favorite clustering tool.

My favourite clustering software is R. Some people may disagree about the 'easy to use' part but once you get over the initial slope of the learning curve it is very easy and hugely powerful. No other tool can really compare in my opinion. However if R is not for you then Cluster 3.0 and MapleTree are the way forward.

I am currently using Cluster 3.0 for clustering and TreeView.

I would recommend a combination of cluster and treeview.

pretty powerful!

Possibly related: http://mmc.gnets.ncsu.edu/

One thing you might look at is the Broad Institute's genepattern software. It can be clunky at times but it will do most common tasks in a fairly straightforward fashion.

I use TM4 MultiExperiment Viewer (MeV), SMD and Eisen's Cluster3 with treeview. MeV has more capabilities to handle the microarray data.

Microarray Resources : Software and Tools

You may also try EXPANDER and SEURAT

One thing you might look at is the Broad Institute's genepattern software. It can be clunky at times but it will do most common tasks in a fairly straightforward fashion herve leger