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Unordered Q matricesExamples of Q matrices (equal rates) used to simulate an unordered evolutionary trajectory. Character evolution was modelled using a continuous-time Markov model, where each transition between character states is assigned an instantaneous rate.
| State 1 | State 2 | State 3 | State 4 | |
|---|---|---|---|---|
| Reversible Q matrix | ||||
| State 1 | –3 | 1 | 1 | 1 |
| State 2 | 1 | –3 | 1 | 1 |
| State 3 | 1 | 1 | –3 | 1 |
| State 4 | 1 | 1 | 1 | –3 |
| Non-reversible Q matrix | ||||
| State 1 | –3 | 1 | 1 | 1 |
| State 2 | 0 | –2 | 1 | 1 |
| State 3 | 0 | 0 | –1 | 1 |
| State 4 | 0 | 0 | 0 | 0 |
