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Bioinformatics. 2000 Nov;16(11):1003-9.

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

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Rice University, HiPerSoft, MS-41, 6100 S. Main, Houston, Texas 77005, USA.


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.


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


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