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Bioinformatics Advance Access published online on January 17, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl643
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

TreeQ-VISTA: An Interactive Tree Visualization Tool with Functional Annotation Query Capabilities

Shengyin Gu 1, Iain Anderson 2, Victor Kunin 2, Michael Cipriano 3, Simon Minovitsky 3, Gunther Weber 1, Nina Amenta 1, Bernd Hamann 1 and Inna Dubchak *,2,3

1 Institute for Data Analysis and Visualization (IDAV), Department of Computer Science, University of California, Davis, One Shields Ave., Davis, CA 95616, USA
2 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
3 Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA

*To whom correspondence should be addressed. Inna Dubchak, E-mail: vista{at}lbl.gov


  Abstract

Summary: We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic properties, are interactively queried from a user-provided relational database with a user-friendly interface which provides a set of tools for users with or without SQL knowledge. The query results are projected onto a phylogenetic tree and can be displayed in multiple color groups. A rich set of browsing, grouping and query tools are provided to facilitate trait exploration, comparison and analysis.

Availability: The program, detailed tutorial and examples are available online at http://genome-test.lbl.gov/vista/TreeQVista.

Associate Editor: Chris Stoeckert

Received on November 8, 2006; revised on December 14, 2006; accepted on December 16, 2006

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