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

Figure 4

Comparative analysis of the Bacillus cereus group.

A heat-plot based on a 200/100 BLASTN fragmented alignment without threshold is shown. The figure is cropped to show only the Bacillus cereus group. Target groups used for PCR design are indicated (T1–T5). All remaining Bacillus genomes were used as a background group. This analysis was made without a threshold to filter non-conserved genetic material. Viewing the heat-plot without a threshold means that the values are based on both the core genome size and the core conservation. This often gives a better view during target group formulation because signatures are per definition outside the core when comparing a target genome with a background genome. Insert A shows the uniqueness signature for B. anthracis (T1). Signatures for all groups are present in Figure S3. Insert B shows a dendrogram based on the heat plot. The dendrogram was produced in SplitsTree 4 (using neighbor joining method) made from a distance matrix Nexus file exported from Gegenees. B. cytotoxicus was set as outgroup.

Figure 4