The Open Source Clustering Software consists of the most commonly used routines for clustering analysis of gene expression data. The software packages below all depend on the C Clustering Library, which is a library of routines for hierarchical (pairwise single-, complete-, maximum-, and average-linkage) clustering, k-means clustering, and Self-Organizing Maps on a 2D rectangular grid. The C Clustering Library complies with the ANSI C standard.
Several packages are available as part of the Open Source Clustering Software: * Cluster 3.0 is a GUI-based program for Windows, based on Michael Eisen's Cluster/TreeView code. Cluster 3.0 was written for Microsoft Windows, and subsequently ported to Mac OS X (Cocoa) and Unix/Linux. Cluster 3.0 can also be used as a command line program. * Pycluster (or Bio.Cluster if used as part of Biopython) is an extension module to the scripting language Python. * Algorithm::Cluster is an extension module to the scripting language Perl. * The routines in the C Clustering Library can also be used directly by calling them from other C programs.
See the INSTALL file in this directory.
We recommend using Java TreeView for visualizing clustering results. Java TreeView is a Java version of Michael Eisen's Treeview program with extended capabilities. In particular, it is possible to visualize k-means clustering results in addition to hierarchical clustering results.
Java TreeView was written by Alok Saldanha at Stanford University; it can be downloaded at http://jtreeview.sourceforge.net.
The routines in the C Clustering Library is described in the manual
(cluster.pdf). This manual also describes how to use the routines from Python
and from Perl. Cluster 3.0 has a separate manual (cluster3.pdf). Both of these
manuals can be found in the doc subdirectory. They can also be downloaded from
our website:
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/cluster.pdf;
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/cluster3.pdf.
M.J.L. de Hoon, S. Imoto, J. Nolan, and S. Miyano: "Open Source Clustering Software", Bioinformatics 20(9): 1453-1454 (2004).
Michiel de Hoon
University of Tokyo, Institute of Medical Science
Human Genome Center, Laboratory of DNA Information Analysis
Currently at
RIKEN Genomic Sciences Center
mdehoon 'AT' gsc.riken.jp