Phylogenomic overview in Gegenees.

<p>Both heat-plots of the similarity matrices and trees created from the same data are shown. <b>A</b>. A Gegenees heat-plot over a set of <i>Bacillus</i> strains that had previously been analyzed by MLST <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039107#pone.0039107-Kolsto1" target="_blank">[17]</a>. The heat-plot is based on a fragmented alignment using BLASTN made with settings 200/100. The cutoff threshold for non-conserved material was 30%. A dendrogram was produced in SplitsTree 4 (using neighbor joining method) made from a Nexus file exported from Gegenees. <i>B. cytotoxicus</i> was set as outgroup. The clustering is very similar to previously published trees. The scale bar represents a 1% difference in average BLASTN score similarity. <b>B</b>. A Gegenees heat-plot over a set of yeast genomes that has been analyzed before with different phylogenomic methods. These genomes are more distant from each other and a BLASTN comparison does not resolve them well (data not shown). A fragmented alignment in TBLASTX mode was performed with settings 200/200. The cutoff threshold for non-conserved material was 20%. A dendrogram was produced in SplitsTree 4 (using neighbor joining method) made from a distance matrix Nexus file exported from Gegenees. <i>Y. lipolytica</i> was set as outgroup. The clustering here is also very similar to the previously published trees <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039107#pone.0039107-Jeffroy1" target="_blank">[2]</a>. The scale bar represents a 10% difference in average TBLASTX score similarity.