Cluster Analysis and Visualization Software

Cluster and TreeView are an integrated pair of programs for analyzing and visualizing the results of complex microarray experiments. Both written by Michael Eisen.


Michiel de Hoon of the University of Tokyo has created a version of Cluster (called Cluster 3.0) that implements the same algorithms as my software, but will run on Windows XP (and higher), Mac OS X, Linux and UNIX. Please use this version if you have a newer operating system [Download]. The original version of the software is available below, but is no longer being maintained.

[Previous versions]: Perform a variety of types of cluster analysis and other types of processing on large microarray datasets. Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis.Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863. For Windows only, Current version 2.11.

Manual. Source Code. Demo Data.



A C++ command line program that will perform fuzzy k-means clustering on gene expression data. See Gasch AP and Eisen MB (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology 3(11), 1-22.


[Download] [Previous versions]

Graphically browse results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees. Multiple output formats for generation of images for publications. For Windows only.

Current version 1.60. Updated December 6, 2002.



MapleTree is a java-based, open source, cross-platform visualization tool to graphically browse the results of clustering analyses from our Cluster and Fuzzy K clustering software, and many other clustering and analysis programs.

Maple Tree was developed by Lisa Simirenko in our lab.

Commercial use of the ScanAlyze, Cluster and/or TreeView executable and/or source code requries a license from Stanford University. For information on how to obtain a license, please click here.