Table 4 The numbers in the upper diagonal refer to the combined execution time for total HSP calculation, hit sorting and all-vs-all comparison of both strands (forward and reverse) in seconds (acronyms as described in Table 3). The charts in the bottom part are symmetric visual representations of the corresponding cell in the upper diagonal (bar colour legend: blue =GECKO; orange =Gepard; grey =Lastz; and yellow =MUMmer). The total execution time (in seconds) for all the comparisons were: GECKO - 318591, Gepard - 576889, Lastz - 4752315 and MUMmer - 558360. The total time for GECKO represents a dummy execution, the actual execution time (executing the dictionary calculation once) was of 142954
From: Breaking the computational barriers of pairwise genome comparison
| Â | Method | HS | PT | MM | PA | GG | MMU | RN | BT | CF | SS |
|---|---|---|---|---|---|---|---|---|---|---|---|
HS | GECKO | Â | 19190 | 2438 | 11282 | 11433 | 9358 | 11367 | 3768 | 2944 | 5875 |
| Â | Gepard | Â | 6152 | 2581 | 12973 | 2861 | 8644 | 11478 | 5850 | 5540 | 14880 |
| Â | Lastz | Â | 158874 | 140255 | 117398 | 105912 | 108312 | 96593 | 63294 | 70904 | 157619 |
| Â | MUMmer | Â | 13891 | 2536 | 7519 | 11083 | 31164 | 10566 | 2127 | 3277 | 10170 |
PT | GECKO |
| Â | 2932 | 10567 | 9287 | 9686 | 10800 | 3766 | 2939 | 5909 |
| Â | Gepard | Â | Â | 15662 | 22242 | 26400 | 27394 | 9113 | 11362 | 10445 | 12856 |
| Â | Lastz | Â | Â | 135093 | 191012 | 181386 | 210949 | 164312 | 171510 | 146315 | 115160 |
| Â | MUMmer | Â | Â | 6214 | 23434 | 43301 | 27051 | 9640 | 1594 | 2836 | 10384 |
MM | GECKO |
|
| Â | 3322 | 5432 | 5306 | 7558 | 4461 | 3294 | 6387 |
| Â | Gepard | Â | Â | Â | 16356 | 16675 | 15573 | 9349 | 8663 | 7111 | 13517 |
| Â | Lastz | Â | Â | Â | 141032 | 128324 | 136632 | 128874 | 72552 | 57393 | 133667 |
| Â | MUMmer | Â | Â | Â | 4512 | 6669 | 17013 | 25387 | 1736 | 6005 | 10423 |
PA | GECKO |
|
|
| Â | 31137 | 10012 | 5907 | 3770 | 3081 | 5879 |
| Â | Gepard | Â | Â | Â | Â | 28282 | 25929 | 11305 | 11727 | 11680 | 14778 |
| Â | Lastz | Â | Â | Â | Â | 148768 | 167206 | 135357 | 82444 | 63000 | 157305 |
| Â | MUMmer | Â | Â | Â | Â | 15115 | 36458 | 19321 | 3330 | 3170 | 11564 |
GG | GECKO |
|
|
|
| Â | 9703 | 5957 | 5206 | 5294 | 7895 |
| Â | Gepard | Â | Â | Â | Â | Â | 25819 | 9960 | 13355 | 13250 | 13244 |
| Â | Lastz | Â | Â | Â | Â | Â | 137351 | 63414 | 44411 | 28089 | 66732 |
| Â | MUMmer | Â | Â | Â | Â | Â | 36614 | 11729 | 6869 | 30429 | 45431 |
MMU | GECKO |
|
|
|
|
| Â | 5908 | 5159 | 5170 | 5873 |
| Â | Gepard | Â | Â | Â | Â | Â | Â | 10229 | 12219 | 11360 | 13493 |
| Â | Lastz | Â | Â | Â | Â | Â | Â | 58823 | 44641 | 32046 | 92761 |
| Â | MUMmer | Â | Â | Â | Â | Â | Â | 8546 | 1307 | 2756 | 10128 |
RN | GECKO |
|
|
|
|
|
| Â | 5930 | 5894 | 5935 |
| Â | Gepard | Â | Â | Â | Â | Â | Â | Â | 8143 | 6458 | 17278 |
| Â | Lastz | Â | Â | Â | Â | Â | Â | Â | 47869 | 39163 | 79895 |
| Â | MUMmer | Â | Â | Â | Â | Â | Â | Â | 1979 | 4702 | 15277 |
BT | GECKO |
|
|
|
|
|
|
| Â | 3777 | 5914 |
| Â | Gepard | Â | Â | Â | Â | Â | Â | Â | Â | 6574 | 9827 |
| Â | Lastz | Â | Â | Â | Â | Â | Â | Â | Â | 21861 | 56029 |
| Â | MUMmer | Â | Â | Â | Â | Â | Â | Â | Â | 717 | 1608 |
CF | GECKO |
|
|
|
|
|
|
|
| Â | 5889 |
| Â | Gepard | Â | Â | Â | Â | Â | Â | Â | Â | Â | 8302 |
| Â | Lastz | Â | Â | Â | Â | Â | Â | Â | Â | Â | 51778 |
| Â | MUMmer | Â | Â | Â | Â | Â | Â | Â | Â | Â | 2777 |
SS | GECKO |
|
|
|
|
|
|
|
|
| Â |
| Â | Gepard | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
| Â | Lastz | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
| Â | MUMmer | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
