UPGMA tree generated from tribeMCL clustering of CDSs from Se4047 prophage (highlighted in red) and S. pyogenes prophage. S. pyogenes prophage used in the clustering were: Manfredo (ϕMan.1, ϕMan.2, ϕMan.3, ϕMan.4, and ϕMan.5), SSI-1 (SPsP1, SPsP2, SPsP3, SPsP4, and SPsP5), SF370 (370.1, 370.2, 370.3, and 370.4), MGAS315 (ϕ315.1, ϕ315.2, ϕ315.3, ϕ315.4, ϕ315.5, and ϕ315.6), MGAS8232 (ϕspeA, ϕspeC, ϕspeL/M, ϕ370.3-like, and ϕsda), MGAS10394 (ϕ10394.1, ϕ10394.2, ϕ10394.3, ϕ10394.4, ϕ10394.5, ϕ10394.6, ϕ10394.7, and ϕ10394.8), MGAS6180 (ϕ6180.1, ϕ6180.2, ϕ6180.3, and ϕ6180.4), MGAS5005 (ϕ5005.1, ϕ5005.2, and ϕ5005.3), MGAS2096 (ϕ2096.1 and ϕ2096.2), MGAS9429 (ϕ9429.1, ϕ9429.2, and ϕ9429.3), MGAS10270 (ϕ10270.1, ϕ10270.2, ϕ10270.3, 10270.4, and 10270.5), and MGAS10750 (ϕ10270.1, ϕ10270.2, ϕ10270.3, and ϕ10270.4). The distribution of homologues to virulence cargo of Se4047 prophage are indicated on the right hand side. CDSs belonging to the same homology groups defined using TribeMCL with a cutoff of 1e−5 are indicated by colored blocks: slaA (yellow), seeM (green), seeL (dark blue), seeH (light blue), and seeI (pink).