Table 1.

Absolute difference between number of gene families determined by NC and those determined by GenFamClust.

		Dataset
	Transl. rate	.0002	.0025	.005	.0002	.0025	.005
	Dupl. rate	.0085	.0085	. 0085	.006	.006	.006
	Subst. rate	100	100	100	250	250	250
Clustering	Algorithm	1	2	3	4	5	6
Average Linkage	NC	83	10	39	1211	552	493
	GenFamClust	32	7	23	751	457	437
Complete Linkage	NC	127	35	68	1316	608	560
	GenFamClust	58	16	53	821	503	489
Single Linkage	NC	59	6	21	1115	502	440
	GenFamClust	6	16	1	631	397	379
Extant gene families	-	329	289	382	241	258	233

Each cell represents the absolute difference between number of extant gene families (observable at leaves) (last row) and the number of gene families determined by the corresponding gene family algorithm for the corresponding dataset with the corresponding linkage algorithm. For NC, the threshold of 0.5 was used while for GenFamClust, the elliptical curve with NC = 0.5 and SyC = 1.0 was used.