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Bioinformatics Advance Access published online on May 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth307
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 29, 2003
Revised March 24, 2004
Accepted April 28, 2004

Applications note

ClutrFree: cluster tree visualization and interpretation

Ghislain Bidaut 1 Michael F. Ochs 2*

1 Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA; Structural and Genomic Information Laboratory, (CNRS UPR2589), 13402 Marseille, France
2 Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA

* To whom correspondence should be addressed. E-mail: Michael.Ochs{at}fccc.edu.


  Abstract

Summary: ClutrFree facilitates the visualization and interpretation of clusters or patterns computed from microarray data through a graphical user interface that displays patterns, membership information of the genes, and annotation statistics simultaneously. ClutrFree creates a tree linking the patterns based on similarity, permitting the navigation among patterns identified by different algorithms or by the same algorithm with different parameters, and aids the inferring of conclusions from a microarray experiment.

Availability: The ClutrFree Java source code and compiled bytecode are available as a package under the GNU General Public License at http://bioinformatics.fccc.edu.

Supplementary Information: Extended documentation on the software usage, as well as supplemental figures and an appropriate test data set are provided on the web site.


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