This is the manual for Cluster 3.0. Cluster was originally written by Michael Eisen while at Stanford University. We have modified the k-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 The proprietary Numerical Recipes routines, which were used in the original version of Cluster/TreeView, have been replaced by open source software.
Cluster 3.0 is available for Windows, Mac OS X, Linux, and Unix.
November 5, 2002.
Michiel de Hoon
Human Genome Center, University of Tokyo.