Table 1.
–freq times (sec)
| Dataset | Machine | PLINK 1.07 | PLINK 1.90 | Ratio |
|---|---|---|---|---|
| synth1 | Mac-2 | 7.3 | 0.24 | 30 |
| Mac-12 | 6.2 | 0.18 | 34 | |
| Linux32-2 | 13.1 | 0.56 | 23 | |
| Linux32-8 | 4.3 | 0.18 | 24 | |
| Linux64-512 | 5.4 | 0.18 | 27 | |
| Win32-2 | 14.3 | 0.68 | 21 | |
| Win64-2 | 9.6 | 0.33 | 29 | |
| synth2 | Mac-2 | 43.3 | 0.84 | 52 |
| Mac-12 | 38.2 | 0.34 | 110 | |
| Linux32-2 | 80.1 | 1.9 | 42 | |
| Linux32-8 | 25.2 | 0.53 | 48 | |
| Linux64-512 | 34.1 | 0.40 | 85 | |
| Win32-2 | 83.6 | 1.3 | 64 | |
| Win64-2 | 70.8 | 0.55 | 130 | |
| chr1snp | Mac-2 | 52.5 | 3.5 | 15 |
| Mac-12 | 40.5 | 1.3 | 31 | |
| Linux32-2 | 72.9 | 10.2 | 7.15 | |
| Linux32-8 | 29.7 | 1.4 | 21 | |
| Linux64-512 | 36.8 | 1.4 | 26 | |
| Win32-2 | 104.3 | 4.5 | 23 | |
| Win64-2 | 76.8 | 2.2 | 35 | |
| chr1 | Mac-2 | 403.9 | 35.0 | 11.5 |
| Mac-12 | 163.9 | 5.3 | 31 | |
| Linux32-2 | nomem | 65.3 | ||
| Linux32-8 | 134.1 | 12.8 | 10.5 | |
| Linux64-512 | 144.7 | 5.4 | 27 | |
| Win32-2 | 389.2 | 21.4 | 18.2 | |
| Win64-2 | 285.3 | 8.1 | 35 |
This command reports allele frequencies for each variant. The computation is trivial, so the timings just reflect program initialization speed and file I/O efficiency.