Table 1. Results of simulation testing.

Results include all simulations with both the MSCM and MSCM+m models. False positives are datasets simulated under the MSCM model which P2C2M.SNAPP classified as a model violation. False negatives are datatsets simulated under the MSCM+m model that P2C2M.SNAPP classified as not violating the model implemented in SNAPP.

Statistic	True positives	True negatives	False positives	False negatives	Matthews correlation coefficient (MCC)
Average pairwise FST (FSTA)	66	0	100	34	−0.45
Range of pairwise FST (FSTR)	81	0	100	19	−0.32
FST outlier test (PFST)	3	88	12	97	−0.17
Kuhner–Felsenstein distance (KF)	100	0	100	0	0.00
Robinson–Foulds distance (RF)	0	100	0	100	0.00
Mean of maximum likelihood (MLM)	84	0	100	16	−0.29
Standard deviation of maximum likelihood (MLSD)	71	95	5	29	0.68