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Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

Figure 3

Phylogenomic overview in Gegenees.

Both heat-plots of the similarity matrices and trees created from the same data are shown. A. A Gegenees heat-plot over a set of Bacillus strains that had previously been analyzed by MLST [17]. 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. B. cytotoxicus 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. 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. Y. lipolytica was set as outgroup. The clustering here is also very similar to the previously published trees [2]. The scale bar represents a 10% difference in average TBLASTX score similarity.

Figure 3

doi: https://doi.org/10.1371/journal.pone.0039107.g003