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Bioinformatics Advance Access published online on May 19, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp330
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

jClust: A clustering and visualization toolbox.

Georgios A. Pavlopoulos 1,#, Charalampos N Moschopoulos 2,#, Sean D. Hooper 3, Reinhard Schneider 1,§,* and Sophia Kossida 2,§,*

1 Structural and Computational Biology Unit, EMBL Meyerhofstrasse 1, Heidelberg, Germany.
2 Bioinformatics & Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, GR-11527, Athens, Greece
3 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

*To whom correspondence should be addressed. Mr. Georgios Pavlopoulos, E-mail: pavlopou{at}embl.de


  Abstract

jClust is a user friendly application which provides access to a set of widely used clustering and clique finding algorithms. The toolbox allows a range of filtering procedures to be applied and is combined with an advanced implementation of the Medusa interactive visualization module. These implemented algorithms are k-Means, Affinity Propagation, Bron-Kerbosch, MULIC, Restricted Neighborhood Search Cluster Algorithm, Markov Clustering and Spectral Clustering while the supported filtering procedures are haircut, outside-inside, best neighbors and density control operations. The combination of a simple input file format, a set of clustering and filtering algorithms linked together with the visualization tool provides a powerful tool for data analysis and information extraction.

Availability and supplementary material: http://jclust.embl.de/

Associate Editor: Dr. Jonathan Wren

# Equal contribution to this work.

§ These authors contributed equally.

Received on March 16, 2009; revised on April 27, 2009; accepted on April 15, 2009

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