Comparing RXNMapper to Indigo (17) and Mappet (16).
| RXNMapper | Indigo (17) | Mappet (16) | |
| Average time (short) | 6.4 ms | 17.0 ms | Slower than Indigo |
| Average time (strongly unbalanced) | 7.7 ms | 2400 ms | Not handled |
| Quality on complex reactions | High | Low | High |
| Quality on strongly unbalanced reactions | High | Low | – |
| Open-source code? | Yes | Yes | No |