Fig. 3.

Classification of prophages. (A) Phylogenetic tree of phages and prophages based on gene repertoire relatedness (see Materials and Methods). Phage/prophage families are colored according to the color key. The phage/prophage genus is indicated in the inner circle. The members of the “lambdoid” group are indicated in the second circle. The classification of phages/prophages into temperate and virulent is indicated in the third circle. White clusters correspond to unclassified clades. (B) Phylogenetic tree as in (A) but restricted to temperate phages/prophages. Red branches correspond to Salmonella phages/prophages and black branches to Escherichia phages/prophages. Labels indicate some types of phages/prophages of interest and mentioned in the text.