PentaPlot: A software tool for the illustration of genome mosaicism

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...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Lutz Hamel, Olga Zhaxybayeva, J. Peter Gogarten
• Keywords: BMCBI 2005, Dekapentagonal Maps, Gene Families, Optimal Layout