Table 3.
Sequence-sequence comparison F-measures for clustered sequences
| Family | ||||
|---|---|---|---|---|
| Dataset | TransClust ( T ) | HiFix ( s,c ) | MCL ( I ) | SCPS ( c ) |
| A-10 | 0.494 (1) | 0.467 (0.10,0.7) | 0.352 (18) | - |
| A-20 | 0.573 (1) | 0.491 (0.15,0.7) | 0.398 (17) | - |
| A-30 | 0.675 (1) | 0.583 (0.20,0.7) | 0.415 (51) | - |
| A-50 | 0.721 (1) | 0.608 (0.25,0.7) | 0.457 (40) | - |
| A-70 | 0.739 (1) | 0.630 (0.25,0.7) | 0.474 (30) | - |
| A-90 | 0.758 (1) | 0.653 (0.25,0.7) | 0.511 (29) | - |
| A-95 | 0.766 (1) | 0.654 (0.25,0.7) | 0.527 (22) | - |
| GOLD | 0.914 (25) | 0.902 (0.30,0.6) | 0.880 (12) | - |
| Super-family | ||||
| A-10 | 0.377 (1) | 0.337 (0.10,0.7) | 0.270 (18) | 0.297 (648) |
| A-20 | 0.450 (1) | 0.362 (0.10,0.7) | 0.282 (18) | 0.352 (753) |
| A-30 | 0.551 (1) | 0.473 (0.10,0.7) | 0.333 (57) | 0.473 (955) |
| A-50 | 0.609 (1) | 0.507 (0.25,0.7) | 0.351 (59) | 0.557 (1188) |
| A-70 | 0.631 (1) | 0.539 (0.25,0.7) | 0.377 (43) | 0.581 (1279) |
| A-90 | 0.654 (1) | 0.560 (0.25,0.7) | 0.426 (43) | 0.607 (1345) |
| A-95 | 0.659 (1) | 0.563 (0.25,0.7) | 0.435 (28) | 0.615 (1401) |
| GOLD | 0.865 (1) | 0.915 (0.05,0.3) | 0.827 (36) | 0.904 (6) |
The optimized set of parameters determined for each clustering algorithm are shown in parenthesis, see Section ‘Parameter optimization’. Best values are shown in bold.