Table 2. Performance of different algorithms for 5-way network alignment.

	DMC			DMR			CG
	SPE	CN	MNE	SPE	CN	MNE	SPE	CN	MNE
SMETANA	91.21	7299	6.94	91.55	7203	7.13	93.60	7359	5.51
IsoRankN	80.91	5538	10.27	79.58	5496	11.14	82.68	5689	9.72
NBM	85.17	1038	5.40	79.32	1182	6.81	84.62	1995	4.64
Græmlin 2.0	51.07	3028	16.32	50.88	3100	16.94	62.89	4451	13.19
SMETANA (only 5-species)	89.07	4067	4.64	88.93	3712	4.43	92.17	3782	2.66
IsoRankN (only 5-species)	69.67	1859	9.67	68.07	1610	10.26	73.83	2223	7.99
Græmlin 2.0 (only 5-species)	35.90	1575	19.50	36.60	1581	20.29	54.44	2394	14.17

Performance comparison based on the 5-way alignment of five networks of size 1500, 2000, 2500, 3000 and 3000. The last three rows are obtained by considering only equivalence classes that contain at least one node from every species. The performance of each method is assessed using the following metrics: specificity (SP), number of correct nodes (CN), and mean normalized entropy (MNE). In each metrics, best performance is shown in bold.