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Bioinformatics Vol. 16 no. 11 2000
Pages 1003-1009
© 2000 Oxford University Press

Original Paper

Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions

Derek A. Ruths 1, Edward S. Chen 1, and Leland Ellis 2

1 Rice University, HiPerSoft, MS-41, 6100 S. Main, Houston, Texas 77005, USA
2 W. M. Keck Center for Informatics, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, 2121 Holcombe, Houston, Texas, 77030, USA

Received on January 21, 2000 ; revised on April 14, 2000 ; accepted on May 17, 2000

This paper examines a new technique for the visualization of and the interaction with trees, objects frequently used to convey hierarchical relationships in biological data. Motivated by the quality of 2D tree interaction, we adapt the planar tree-of-life metaphor to a virtual, semi-immersive 3D environment. A 3D environment extends the utility of this metaphor by allowing the user to view an entire data set in a single screen. Interrogation of the tree is implemented using 3D input devices. This real-time interrogation of the tree itself provides a quick means by which to qualitatively analyse the hierarchical data. In this paper, we describe the techniques underlying the implementation of such an environment. We conclude by considering the utility of tree metaphors as a basis for the representation of highly dimensional data sets.

Availability: Arbor3D (source code, a binary executable for SGI IRIX 6.4, Perl parsers, and sample Newick data files) are available via the Internet (http://xian.tamu.edu/Arbor3D/). Arbor3D can be displayed in ‘CAVE simulator’ mode on an SGI workstation screen, or as an interactive virtual environment on a projection workbench.

Contact: druths{at}rice.edu; echen{at}cs.rice.edu; leland{at}xian.tamu.edu

To whom correspondence should be addressed.


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