The open source clustering software available here implement the most commonly used clustering methods for gene expression data analysis. The clustering methods can be used in several ways.

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Provides a Graphical User Interface to access to the clustering routines. It is available for Windows, Mac OS X, and Linux/Unix. Python users can access the clustering routines by using, which is an extension module to Python.

People that want to make use of the clustering algorithms in their own C, C++, or Fortran programs can download the of the C Clustering Library. Cluster 3.0 is an enhanced version of Cluster, which was originally developed by while at. Cluster 3.0 was built for the Microsoft Windows platform, and later ported to Mac OS X (Cocoa build for Mac OS X v10.0 or later) and to Linux/Unix using Motif.

In addition to the GUI program, Cluster 3.0 can also be run as a. For more information, please consult the. Installation: For and, use the appropriate installer. The Cluster 3.0 executables cluster.com (on Windows) or Cluster (on Mac OS X) can be used both as a GUI program and as a command line program.

For Cluster 3.0 on Linux/Unix, you will need the Motif libraries, which are already installed on many Linux/Unix computers. You will need a version compliant with Motif 2.1, such as. Cluster 3.0 can then be installed by typing./configure make make install The resulting executable cluster can be run as a GUI program and as a command line program. For the latter, you will need to use the appropriate. If you are not interested in the GUI, and you want to run Cluster 3.0 as a command line program only, you can install a command-line only version of Cluster by typing./configure --without-x make make install If you install Cluster 3.0 as a command-line only program you do not need the Motif libraries. Download ( last update November 22, 2018; C Clustering Library version 1.57):;.

You may need to remove /Library/Receipts/Cluster.pkg if you have an older version of Cluster 3.0 installed. If you get the error message 'Cluster.pkg' can't be opened because it is from an unidentified developer.' , right-click on Cluster.pkg after downloading, and select 'Open With' → 'Installer'.;.

Java TreeView To view the clustering results generated by Cluster 3.0, we recommend using Alok Saldanha's, which can display hierarchical as well as k-means clustering results. Java TreeView is not part of the Open Source Clustering Software.

Is a scripting language with excellent support for numerical work through the package, providing a functionality similar to Matlab and R. This makes Python together with Numerical Python an ideal tool for analyzing genome-wide expression data. Pycluster now uses the 'new' Numerical Python (version 1.3 or later). Python can be easily integrated with C and other low-level languages, thus combining the speed of C with the flexibility of Python. The routines available in Pycluster are described in the. To install Pycluster, download the Pycluster source distribution, unpack, change to the directory Pycluster-1.57, and type python setup.py install as usual.