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Open Access Highly Accessed Software

PhyloFinder: An intelligent search engine for phylogenetic tree databases

Duhong Chen1*, J Gordon Burleigh2, Mukul S Bansal1 and David Fernández-Baca1

Author Affiliations

1 Department of Computer Science, Iowa State University, Ames, IA 50011, USA

2 NESCent, Durham, NC 27705, USA

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BMC Evolutionary Biology 2008, 8:90  doi:10.1186/1471-2148-8-90

Published: 21 March 2008

Abstract

Background

Bioinformatic tools are needed to store and access the rapidly growing phylogenetic data. These tools should enable users to identify existing phylogenetic trees containing a specified taxon or set of taxa and to compare a specified phylogenetic hypothesis to existing phylogenetic trees.

Results

PhyloFinder is an intelligent search engine for phylogenetic databases that we have implemented using trees from TreeBASE. It enables taxonomic queries, in which it identifies trees in the database containing the exact name of the query taxon and/or any synonymous taxon names, and it provides spelling suggestions for the query when there is no match. Additionally, PhyloFinder can identify trees containing descendants or direct ancestors of the query taxon. PhyloFinder also performs phylogenetic queries, in which it identifies trees that contain the query tree or topologies that are similar to the query tree.

Conclusion

PhyloFinder can enhance the utility of any tree database by providing tools for both taxonomic and phylogenetic queries as well as visualization tools that highlight the query results and provide links to NCBI and TBMap. An implementation of PhyloFinder using trees from TreeBASE is available from the web client application found in the availability and requirements section.