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. 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. A command line version
  of this program is also available.
* 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.


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://jtreeview.sourceforge.net.


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
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.


LITERATURE
==========

M.J.L. de Hoon, S. Imoto, J. Nolan, and S. Miyano: "Open Source Clustering
Software", Bioinformatics 20(9): 1453-1454 (2004).


CONTACT
=======

Michiel de Hoon
University of Tokyo, Institute of Medical Science
Human Genome Center, Laboratory of DNA Information Analysis
Currently at
Columbia University, Center for Computational Biology and Bioinformatics
mdehoon@c2b2.columbia.edu