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Bioinformatics Advance Access originally published online on June 4, 2004
Bioinformatics 2004 20(17):2997-3004; doi:10.1093/bioinformatics/bth345
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Visualizations for taxonomic and phylogenetic trees

Cynthia Sims Parr 1,2,*, Bongshin Lee 3, Dana Campbell 1 and Benjamin B. Bederson 3

1 Human-Computer Interaction Lab, University of Maryland, College Park, MD 20742, USA and 2 Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA and 3 Human Computer Interaction Lab, Computer Science Department, University of Maryland, College Park, MD 20742, USA

Received on February 27, 2004; revised on May 3, 2004; accepted on May 25, 2004
Advance Access Publication June 4, 2004

Motivation: Despite substantial efforts to develop and populate the back-ends of biological databases, front-ends to these systems often rely on taxonomic expertise. This research applies techniques from human–computer interaction research to the biodiversity domain.

Results: We developed an interactive node-link tool, TaxonTree, illustrating the value of a carefully designed interaction model, animation, and integrated searching and browsing towards retrieval of biological names and other information. Users tested the tool using a new, large integrated dataset of animal names with phylogenetic-based and classification-based tree structures. These techniques also translated well for a tool, DoubleTree, to allow comparison of trees using coupled interaction. Our approaches will be useful not only for biological data but as general portal interfaces.

Availability: Working versions of TaxonTree and DoubleTree and video demonstrations of DoubleTree are available at http://www.cs.umd.edu/hcil/biodiversity

Supplementary information: All datasets and folk tree illustration are available at http://www.cs.umd.edu/hcil/biodiversity

Contact: csparr{at}umd.edu

* To whom correspondence should be addressed.


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[Abstract] [Full Text] [PDF]


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