Open source clustering software

• Published in: Bioinformatics Vol. 20; no. 9; pp. 1453 - 1454
• Main Authors: de Hoon, M.J.L., Imoto, S., Nolan, J., Miyano, S.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 12.06.2004; Oxford Publishing Limited (England)
• Subjects: Algorithms; Biological and medical sciences; Cluster Analysis; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Pattern Recognition, Automated - methods; Programming Languages; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software; Bioinformatics; Software
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bth078

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. Availability: The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.