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PentaPlot

A Software Tool for the Illustration of Genome Mosaicism

 dekapentagon
Project Info Page

Genome Biology Background Paper

Description:

Trees representing the evolutionary history of organisms have been used as models for their phylogenetic relationships since Darwin's time.  However, it is becoming evident that evolutionary trees are not always a good model for the phylogenetic relationships among genomes, particularly microbial genomes, due to the mosaic nature of these genomes.  That is, it seems that the individual genes that make up a genome have different evolutionary histories.  In particular, horizontal gene transfer is recognized as an alternative to within lineage processes like duplication and de-novo evolution of genes for an organism to acquire new properties.  This software tool computes dekapentagonal maps to depict the phylogenetic relationships of five genomes in a visually appealing diagram as an alternative to evolutionary trees.  Since these maps are easily interpreted, they can serve as a visual tool to screen for genes that were horizontally transferred between divergent organisms. Dekapentagonal maps allow for the recognition of a plurality or majority signal and they point towards instances of genome fusion.

PentaPlot is written as a program which is comprised of multiple processing steps implemented both in Perl and C++.  The implementation heavily relies on Wall's genetic algorithm C++ component library (http://lancet.mit.edu/ga) and TeX.  The various processing steps are hidden from the average user by means of a master Perl script that ties all the processing steps together.  In normal usage the user prepares a specially formatted probability matrix which provides information about the support of the orthologous gene families for various tree topologies.  This matrix is processed by the program into the visual display of the dekapentagonal map.  The visual display is available in an interactive previewer as well as in the post-script and pdf formats.
Developed by:
J. Peter Gogarten
Olga Zhaxybayeva
Lutz Hamel

Required Software:

In addition to the PentaPlot software you will need to install the following software packages on you Linux system:




(c) copyright 2004