Open Source Clustering Software =============================== 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. As of version 1.04, 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. * Pycluster 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. INSTALLATION ============ See the INSTALL file in this directory. VIEWING CLUSTERING RESULTS ========================== 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://genome-www.stanford.edu/~alok/TreeView. Java TreeView can be started from Cluster 3.0 by pressing the 'Launch JavaTreeView' button. See the installation instructions in INSTALL. MANUAL ====== 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. Cluster 3.0 has a separate manual (ctv.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/ctv.pdf. http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/cluster.pdf. CONTACT ======= Michiel de Hoon, University of Tokyo, Human Genome Center mdehoon@ims.u-tokyo.ac.jp