GPX: A Tool for the Exploration and Visualization of Genome Evolution

Ever since Darwin the Tree of Life has provided a framework to study the evolution of organisms. However, comparative genome analyses of microorganisms have shown that genomes are mosaics where different parts have different histories. This is due to horizontal gene transfer that transforms the Tree of Life into a Web of Life where different parts of a genome possess different evolutionary histories. Clustering gene families based on the phylogenetic information they retain allows extracting a majority consensus for the genomes' evolution, and the determination of genes that have a conflicting phylogeny. The latter is of interest in the context of comparative genomics of prokaryotes because these conflicts point towards possible horizontal transfers of genes and metabolic pathways between divergent organisms. We have created a web-based tool gene phylogeny eXplorer, GPX (http://www.bioinformatics.cs.uri.edu/gpx/) that facilitates comparative genome analysis of different species. GPX displays results as an interactive map that allows users to explore and interpret genomic data representing gene evolution. It allows the visualization of consensus and conflicting evolutionary histories of genes which in turn supports the visual identification of possible horizontal gene transfer events. The novel aspect of our approach is that we do not try to analyze DNA sequences directly but instead use self-organizing maps to find structure (clusters) in a space spanned by all possible evolutionary relationships between the genomes in questions.