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

