Skip Navigation


Bioinformatics Advance Access originally published online on May 19, 2009
Bioinformatics 2009 25(15):1994-1996; doi:10.1093/bioinformatics/btp330
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
25/15/1994    most recent
btp330v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Pavlopoulos, G. A.
Right arrow Articles by Kossida, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pavlopoulos, G. A.
Right arrow Articles by Kossida, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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,*,{dagger}, Charalampos N. Moschopoulos 2,{dagger}, Sean D. Hooper 3, Reinhard Schneider 1,*,{dagger} and Sophia Kossida 2,*,{dagger}

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 and 3 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598, US

* To whom correspondence should be addressed.


  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: http://jclust.embl.de/

Contact: pavlopou{at}embl.de; rschneid{at}embl.de; skossida{at}bioacademy.gr

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors and the last two authors should be regarded as joint Last Authors.

Associate Editor: Jonathan Wren

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.