Exploration of Novel Methods to Visualize Genome Evolution

Goal of our research is to develop and test approaches that can be used to visualize and dissect the mosaic nature of genomes. This will allow tracing histories of individual genes, detection of co-evolving traits, and correlation of the molecular record with the fossil and geological records. In the past we have developed tools that map the support of individual gene families for the different possible phylogenetic trees. However, because of the huge number of possible trees topologies, this approach cannot readily be extended to the depiction of many genomes. To facilitate the processing of phylogenetic information, we will organize the data from analyses of multiple genomes into matrices. For each gene family we will utilize either the significantly supported bipartitions, or the support for the different quartets that can be formed by selecting four of the analyzed species. All of these data matrices will be of very high dimension ([number of orthologous genes] x [number of possible tree topologies / quartets / bipartitions]).