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Bioinformatics Vol. 18 no. 1 2002
Pages 109-114
© 2002 Oxford University Press

TreeWiz: interactive exploration of huge trees

Ursula Rost 1 and Erich Bornberg-Bauer 2,*

1 Bioinformatics and Computational Biochemistry Group, European Media Laboratory GmbH, Schloß-Wolfsbrunnenweg 33, D-69118, Heidelberg, Germany
2 School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road M13 9PT, Manchester, UK

Received on ; revised on July 9, 2001 ; accepted on August 13, 2001

Motivation: The rapidly increasing amount and disparity of biological data requires interpretation at many levels of description. Human judgement and intuition are important because not all data can be automatically and comprehensively analyzed. Visualization of trees and substructures corresponding to certain features are often used to analyze phylogenies or taxonomies. Unfortunately, most existing tools do not cope with the size of current datasets, the required functionality, or both.

Results: We introduce a program for visualization of huge trees and also for the interactive exploration of their content. We have developed a range of new schemes which are tailored for biological problems. Users can get an overview, zoom in, filter out data and retrieve details from standard databases such as SWISS-PROT. Furthermore, it is possible to analyze the relationship between chosen leaf sets that are specified by common features on a second level of representation. On a PC (with {approx} 512 MB RAM), trees of up to several tens of thousands of leaves can be loaded and both rapidly and interactively explored. We demonstrate the use of this program for the analysis of the SYSTERS data set (which contains hierarchically clustered protein sequences) to which PFAM domains were added as features.

Availability: TreeWiz is written in JAVA and is free for academic use. The full application as well as a restricted applet version can be found on the web-page http://www.eml.org/english/staff/homes/ulla/rost.html.

Contact: Ursula.Rost{at}eml.villa-bosch.de

* To whom correspondence should be addressed.


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