Table 3.

Evaluated algorithms and the range of parameters that have been tested.

		Test range
Algorithm	Parameter	Min.	Max.	Step size	Best case
O-HARP	t – cluster tightness	0.1	0.9	0.04	0.58
	f – filtering threshold	0	0.04	0.8	0.24
HARP	K – target # of clusters	3	30	1	7
	MOP – max. outlier percentage	5	13	1	9
SAMBA	v – version	(discrete: 6 versions – tested all)			v2
	t – try covering all probes	(discrete: true/false – tested both)			true
	f – overlap factor	0.001	0.13	varies	0.03
	rp – responding probes to hash	3	30	3	9
Cheng-Church	d – delta	0.03	0.9	varies	0.07
	a – alpha	1.0	1.2	0.1	1.2
	K – target # of clusters	10	300	varies	70
FastDOC	K – target # of clusters	3	18	3	n/a
	b – beta	0.2	0.45	0.05	n/a
	w – cluster width	0.05	0.65	0.2	n/a
	MAXITER – max. # of inner iterations	8000	10000	2000	n/a
SynFPS	K – target # of clusters	5	10	1	9
n-gram	n – length of nucleotide sequence	2	6	1	5
	k – target # of clusters	3	10	1	9