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1 Introduction

Cluster and TreeView are programs that provide a computational and graphical environment for analyzing data from DNA microarray experiments, or other genomic datasets. The program Cluster can organize and analyze the data in a number of different ways. TreeView allows the organized data to be visualized and browsed.

This manual is intended as a reference for using the software, and not as a comprehensive introduction to the methods employed. Many of the methods are drawn from standard statistical cluster analysis. There are excellent textbooks available on cluster analysis which are listed in the bibliography at the end. The bibliography also contains citations for recent publications in the biological sciences, especially genomics, that employ methods similar to those used here.