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Open Access Software

PentaPlot: A software tool for the illustration of genome mosaicism

Lutz Hamel1, Olga Zhaxybayeva23 and J Peter Gogarten2*

Author Affiliations

1 Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI 02881, USA

2 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA

3 Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 1X5, Canada

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BMC Bioinformatics 2005, 6:139  doi:10.1186/1471-2105-6-139

Published: 6 June 2005

Abstract

Background

Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix.

Results

The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families.

Conclusion

PentaPlot is being made publicly available as an open source project at http://pentaplot.sourceforge.net webcite.