Get the latest version: paraclu-9.zip
Paraclu finds clusters in data attached to sequences. It was first applied to transcription start counts in genome sequences, but it could be applied to other things too.
Paraclu is intended to explore the data, imposing minimal prior assumptions, and letting the data speak for itself.
One consequence of this is that paraclu can find clusters within clusters. Real data sometimes exhibits clustering at multiple scales: there may be large, rarefied clusters; and within each large cluster there may be several small, dense clusters.
The original paraclu is a perl script, which is available here. The new version works identically to the original, but is much faster and copes with much bigger data.
For more details, please see: A code for transcription initiation in mammalian genomes, MC Frith, E Valen, A Krogh, Y Hayashizaki, P Carninci, A Sandelin, Genome Research 2008 18(1):1-12.