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<h1 class="settitle" align="center">Cluster 3.0 for Windows, Mac OS X, Linux, Unix</h1>


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<h1 class="node-heading">Top</h1>
<p>This is the manual for Cluster 3.0. Cluster was originally written by Michael Eisen while at Stanford University. We have modified the
<i>k</i>-means
 clustering algorithm in Cluster, and extended the algorithm for Self-Organizing Maps to include two-dimensional rectangular grids. The Euclidean distance and the city-block distance were added as new distance measures between gene expression data. The proprietary Numerical Recipes routines, which were used in the original version of Cluster/TreeView, have been replaced by open source software.
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<p>Cluster 3.0 is available for Windows, Mac OS X, Linux, and Unix.
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<br>
<br>
<p>November 5, 2002.<br>
Michiel de Hoon<br>
Human Genome Center, University of Tokyo.
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<table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">&bull; <a href="Introduction.html#Introduction" accesskey="1">Introduction</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">The purpose of Cluster/TreeView.
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<tr><td align="left" valign="top">&bull; <a href="Data.html#Data" accesskey="2">Data</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">Loading, filtering and adjusting data in Cluster.
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<tr><td align="left" valign="top">&bull; <a href="Distance.html#Distance" accesskey="3">Distance</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">The distance/similarity measures that are available in Cluster.
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<tr><td align="left" valign="top">&bull; <a href="Cluster.html#Cluster" accesskey="4">Cluster</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">The various clustering algorithms implemented in Cluster.
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<tr><td align="left" valign="top">&bull; <a href="Command.html#Command" accesskey="5">Command</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">A command-line (non-GUI) version of Cluster 3.0 is now available.
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<tr><td align="left" valign="top">&bull; <a href="TreeView.html#TreeView" accesskey="6">TreeView</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">Visualize hierarchical clustering results with Java TreeView.
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<tr><td align="left" valign="top">&bull; <a href="Development.html#Development" accesskey="7">Development</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">Information on how to compile Cluster from the source code.
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<tr><td align="left" valign="top">&bull; <a href="Bibliography.html#Bibliography" accesskey="8">Bibliography</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">The bibliography provides references to background information on clustering techniques, as well as some examples of recent biological research in which clustering techniques are applied.
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<tr><td align="left" valign="top">&bull; <a href="Contents.html#Contents" accesskey="9">Contents</a></td><td>&nbsp;&nbsp;</td><td align="left" valign="top">
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