Table 2.
Runtime comparison of programs
| App-SpaM |
RAPPAS |
APPLES | EPA-ng | EPA | pplacer | |||
|---|---|---|---|---|---|---|---|---|
| w = 12 | w = 16 | k = 6 | k = 8 | |||||
| CPU-652 | ||||||||
| Pre-proc. | — | — | 651 | 7253 | 3437 | 3437 | 3437 | 3437 |
| Placement | 152 | 79 | 710 | 454 | 2804 | 1315 | 194338 | 9257 |
| Total | 152 | 79 | 1361 | 7707 | 6241 | 4752 | 197775 | 12694 |
| CPU-512 | ||||||||
| Pre-proc. | — | — | 1070 | 12144 | 1879 | 1879 | 1879 | 1879 |
| Placement | 34 | 22 | 254 | 185 | 348 | 127 | 6626 | 1976 |
| Total | 34 | 22 | 1324 | 12329 | 2227 | 2006 | 8505 | 3855 |
Notes: Comparison of runtimes for all tested programs on two datasets. 10 000 queries were placed for CPU-512 and 100 000 queries for CPU-652. All runtimes are shown in seconds. For each dataset, we show the time for pre-processing (pre-proc.), placement and the total sum of pre-processing and placement with default parameters. Pre-processing includes generating the query alignment or building the phylo-k-mer database for RAPPAS.