Table 3.
Running times on the DGINN validation dataset. For each gene, the running time of ‘Steps 1–7’ and of ‘Step 8’ (Figure 1) is shown. For Step 8 (positive selection analyses), the running time of each method is further shown in Supplementary Table S2. Times for Step 8 are only shown for the query genes of the validation dataset following attribution of orthologous groups (Table 4). The last column of the Table corresponds to the option that best balances running times, sensitivity and specificity; i.e. phylogenetics (Steps 1–7) and positive selection analyses (Step 8) using Bio++ M1NS versus M2NS and M7NS versus M8NS only.
| Steps 1 – 7 | Step 8 | Balance speed and results (steps 1–7, step 8: Bio++ only) | |
|---|---|---|---|
| APOBEC3F | 12:18:39 | 04:11:18 | 14:56:01 |
| FOXP2 | 05:26:33 | 5 days, 23:28:04 | 08:38:01 |
| GADD45A | 01:24:26 | 02:17:59 | 01:57:40 |
| GBP5 | 14:04:30 | 06:43:06 | 15:23:34 |
| GMPR | 03:51:52 | 07:50:42 | 04:43:41 |
| HERC5 | 04:03:01 | 15:36:40 | 07:24:32 |
| IFI16 | 05:45:16 | 5 days, 8:01:45 | 08:35:56 |
| ISG20 | 01:34:50 | 08:01:08 | 02:14:25 |
| MX1 | 02:34:42 | 1 day, 18:16:17 | 07:07:03 |
| NT5C3A | 00:53:48 | 4 days, 20:17:21 | 2 days, 02:23:19 |
| RB1 | 00:14:09 | 14:16:03 | 02:22:44 |
| RHO | 00:06:30 | 02:05:53 | 00:46:35 |
| RSAD2 | 01:11:31 | 18:40:09 | 02:54:29 |
| SAMHD1 | 00:51:44 | 3 days, 13:26:08 | 04:22:11 |
| SERINC3 | 01:21:46 | 11:55:16 | 04:36:03 |
| SHH | 01:54:44 | 06:12:50 | 03:02:32 |
| SMC6 | 02:48:41 | 2 days, 20:34:48 | 06:29:27 |
| TREX1 | 01:01:04 | 09:43:10 | 03:09:30 |
| ZC3HAV1 | 02:38:52 | 2 days, 13:27:12 | 08:39:59 |