Table 4.
Profile-profile comparison F-measures for clustered sequences
| Family | ||||
|---|---|---|---|---|
| Dataset | TransClust ( T ) | HiFix ( s,c ) | MCL ( I ) | SCPS ( c ) |
| A-10 | 0.741 (15) | 0.652 (0.10,0.7) | 0.693 (26) | - |
| A-20 | 0.749 (15) | 0.685 (0.15,0.7) | 0.703 (24) | - |
| A-30 | 0.750 (15) | 0.695 (0.15,0.7) | 0.707 (24) | - |
| A-50 | 0.751 (20) | 0.702 (0.20,0.7) | 0.709 (18) | - |
| A-70 | 0.753 (20) | 0.713 (0.20,0.6) | 0.712 (17) | - |
| A-90 | 0.767 (15) | 0.717 (0.20,0.6) | 0.715 (17) | - |
| A-95 | 0.769 (15) | 0.725 (0.20,0.7) | 0.743 (17) | - |
| GOLD | 0.959 (50) | 0.921 (0.30,0.6) | 0.925 (15) | - |
| Super-family | ||||
| A-10 | 0.722 (1) | 0.699 (0.10,0.6) | 0.752 (59) | 0.750 (648) |
| A-20 | 0.783 (5) | 0.701 (0.10,0.7) | 0.754 (59) | 0.759 (753) |
| A-30 | 0.809 (5) | 0.705 (0.10,0.7) | 0.778 (59) | 0.777 (955) |
| A-50 | 0.827 (5) | 0.710 (0.15,0.7) | 0.781 (58) | 0.789 (1188) |
| A-70 | 0.833 (5) | 0.711 (0.15,0.7) | 0.788 (60) | 0.792 (1279) |
| A-90 | 0.835 (5) | 0.715 (0.15,0.7) | 0.805 (59) | 0.805 (1345) |
| A-95 | 0.837 (5) | 0.716 (0.15,0.7) | 0.807 (60) | 0.805 (1401) |
| GOLD | 0.999 (1) | 0.974 (0.05,0.5) | 1.000 (60) | 1.000 (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.