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A tool called Phamerator is used to display phage maps. The genome is cut into four pieces to display here. Each protein is represented by a rectangle above or below the genome ruler. Proteins are displayed on the top of the genome ruler if they are transcribed from the forward strand, and proteins on the bottom are transcribed from right to left.

This image is a Network phylogeny made in a tool called Splitstree. Each grouping is based on presence and absence of protein phams, not the sequences, the network is from a big database of Bacillus phage genomes containing approximately 265 Bacillus Phages.

Figure 1 shows the gene map of a Bacillus phage named YungSlug. The genome of YungSlug was annotated in Spring 2020 by students in the VCU Phage Lab. It is part of the Helleviridae family, all are myoviral particle morphology with large genomes (200+ genes). It contains 150,011 base pairs, in which the genes are tightly spaced, which leaves little non-coding space. There are 227 predicted protein coding genes, 115 of which are novel to YungSlug. Protein are organized into color-coded phamilies based on a greater than 32.5% sequence identity to one other member of the pham. We use these pham memberships and not sequence as the basis of analysis of proteins in a set of sort-of related genomes.

Splitstree including subspecies of bacillus phages

Figure 2 shows the relation of a large database of Bacillus phages. Splitstree works by grouping genomes based on shared protein presence. The center of the splitstree shows the areas in which the proteins are grouped, or shared, and they are dispersed throughout genomes. The Bacillus with closer relation to each other will be close to each other in the splitstree as well, this has a direct correlation.

Figure 3 is labeled with subspecies of bacillus phages corresponding to figure 2, emphasizes that even though there are different subspecies they are all classified as bacillus phages.