Cluster 3.0 2014.10.07 – Enhanced Version of Cluster

Cluster 3.0 2014.10.07


Cluster 3.0 is an enhanced version of Cluster, which was originally developed by Michael Eisen while at Stanford University.


Cluster is program 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.

The main improvement consists of the k-means algorithm, which now includes multiple trials to find the best clustering solution. This is crucial for the k-means algorithm to be reliable.The routine for self-organizing maps was extended to include 2D rectangular geometries. The Euclidean distance and the city-block distance were added to the available measures of similarity.


Michiel de Hoon of the University of Tokyo



  • Windows
  • Mac OS X
  • Linux/Unix with Motif




Reference: M. J. L. de Hoon, S. Imoto, J. Nolan, and S. Miyano: 
Open Source Clustering Software
Bioinformatics20 (9): 1453–1454 (2004).

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