Table 2.

Results for Rfam and small ncRNA benchmark set

			Quality (MERGED)		Time (in s)
i	#Seq	#C	F	Rand	Phase 4	Timei	TimeALL
Rfam benchmark
0						8314	8314
1	271	5	0.882	0.888	458	14 995	23 309
2	629	14	0.834	0.932	416	19 962	43 272
3	1076	23	0.868	0.956	334	15 108	58 380
7	2181	58	0.877	0.985	154	11 964	104 940
15	2821	130	0.834	0.984	77	2491	129 626
Small ncRNA benchmark
0						720	720
1	140	10	0.942	0.945	42	2434	3154
2	232	20	0.926	0.939	27	3395	6549
3	270	26	0.936	0.935	17	7681	14 230
7	329	35	0.890	0.897	5	250	23 186
15	360	43	0.858	0.866	1	92	24 301

Results for each iteration i on the MERGED partition. Clustering quality is given as F measure and Rand index. The total number of clustered sequences is indicated with #Seq. The total number of clusters after merging is given by #C. Time_i denotes the total time for iteration i, Time_ALL is the total serial time up to iteration i.