Table 2.

Performance of MOPHY in capturing the topology of underlying phylogeny for simulated networks.

Most Specific Modules
	Diameter
	2			3			4
Coverage	MOPHY	Random	p-value	MOPHY	Random	p-value	MOPHY	Random	p-value
20%	1.6**	11.2	0.0039	1.6**	11.2	0.0039	1.6**	12.0	0.0029
40%	1.6**	12.0	0.0013	1.6**	10.8	0.0093	1.6**	12.0	0.0014
60%	1.6**	11.2	0.0019	1.6**	11.6	0.0039	1.6**	11.6	0.0021
Most Comprehensive Modules
	Diameter
	2			3			4
Coverage	MOPHY	Random	p-value	MOPHY	Random	p-value	MOPHY	Random	p-value
20%	2.4**	11.6	0.0048	2.8**	10.8	0.0088	4.4*	10.8	0.0121
40%	2.8**	12.0	0.0036	2.8**	10.8	0.0032	4.4*	10.4	0.0179
60%	1.6**	10.8	0.0062	2.4**	11.2	0.0029	3.6**	10.0	0.0054

Performance of MOPHY in capturing the topology of underlying phylogeny for simulated networks. For each parameter setting, the symmetric distance between the underlying tree and the tree reconstructed by MOPHY/randomized method is shown. Reported values are averages over five runs. p-values indicate the statistical significance of the performance difference between MOPHY and the randomized method. **: p < 0.01, *: p < 0.05.