Total Number of Events in the Tree for Different HGT Penalties
| Archaea HGT penalty | Gene loss | Gene duplication | Genesis | Horizontal gene transfer | Vertically inherited genes | Gene fusion |
| 1 | 1894 | 1164 | 3120 | 1153 | 13285 | 221 |
| 2 | 2805 | 1164 | 3134 | 599 | 14486 | 221 |
| 3 | 3798 | 1164 | 3138 | 257 | 15501 | 221 |
| 4 | 4826 | 1164 | 3138 | 0 | 16529 | 221 |
| Proteobacteria HGT penalty | Gene loss | Gene duplication | Genesis | Horizontal gene transfer | Vertically inherited genes | Gene fusion |
| 1 | 9815 | 3684 | 5337 | 3181 | 24160 | 747 |
| 2 | 11201 | 3684 | 5337 | 2483 | 25546 | 747 |
| 3 | 11717 | 3677 | 5341 | 2289 | 26054 | 747 |
| 4 | 13976 | 3666 | 5341 | 1655 | 27689 | 747 |
| 5 | 18761 | 3663 | 5535 | 499 | 30576 | 747 |
| 6 | 18773 | 3663 | 5536 | 495 | 30586 | 747 |
| 7 | 18780 | 3663 | 5536 | 493 | 30591 | 747 |
| 8 | 22636 | 3663 | 5536 | 0 | 32541 | 747 |