|
Evaluated algorithms and the range of parameters that have been tested. |
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| Test range |
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|
|
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| 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 |
|
Li et al. BMC Evolutionary Biology 2008 8:116 doi:10.1186/1471-2148-8-116 |
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