PermutMatrix is a freely available software to explore and visualize gene/protein expression data. It is a very useful tool to cluster genes or proteins according to similarities in their expression profiles.
PermutMatrix can be downloaded from the following link, and the user guide is available here.
1. A software for analysing and visualising data. Caraux G., Pinloche S. Bioinformatics. 2005 21(7):1280-1281
2. Assessment of hierarchical clustering methodologies for proteomic data mining. Meunier et al., J. Proteome Res., 2007, 6 (1), 358–366