Table 3.
Average CPU time* required to calculate one structure alignment of ten different algorithms
| Algorithm | MALIDUP-sq | MALIDUP-ns | MALISAM-sq | MALISAM-ns |
|---|---|---|---|---|
| DaliLite |
0.910s |
1.019s |
0.445s |
0.539s |
| TM-align |
0.111s |
0.087s |
0.055s |
0.043s |
| CE |
0.152s |
— |
0.055s |
— |
| MICAN |
0.134s |
0.134s |
0.098s |
0.097s |
| DEDAL |
5.734s |
6.000s |
0.272s |
0.259s |
| SNAP |
1.517s |
1.743s |
0.962s |
1.128s |
| GANGSTA+ |
0.270s |
0.273s |
0.185s |
0.190s |
| SCALI |
8.272s |
8.153s |
2.723s |
2.870s |
| MASS |
0.138s |
0.136s |
0.105s |
0.106s |
| SAMO | 0.454s | 0.455s | 0.166s | 0.163s |
*CPU times are measured on a PC with Intel Core-i7 2.93 GHz processor.