Table 3.

Performance of MOPHY in capturing the underlying evolutionary distances for simulated networks.

Most Specific Modules
	Diameter
	2			3			4
Coverage	MOPHY	Random	p-value	MOPHY	Random	p-value	MOPHY	Random	p-value
20%	6.87**	16.40	0.0020	6.84**	15.85	0.0017	6.97**	15.78	0.0019
40%	6.81**	16.14	0.0017	6.86**	15.85	0.0017	7.01**	15.53	0.0029
60%	6.79**	15.85	0.0017	6.86**	15.41	0.0016	7.02**	15.25	0.0026
Most Comprehensive Modules
	Diameter
	2			3			4
Coverage	MOPHY	Random	p-value	MOPHY	Random	p-value	MOPHY	Random	p-value
20%	8.89	11.72	0.2283	9.67	11.76	0.3512	10.83	11.82	0.6277
40%	7.62*	13.12	0.0277	8.44	11.61	0.2029	9.63	11.29	0.4922
60%	6.70**	14.93	0.0018	7.92	12.90	0.0529	8.96	11.51	0.3263

For each parameter setting, the nodal distance between the underlying tree and the tree reconstructed by MOPHY/randomized method is shown.