Table 1 displays execution times for plink –freq, one of the simplest operations PLINK can perform. These timings reflect fixed initialization and I/O overhead. (Due to the use of warmup runs, they do not include disk latency).Table 1 –freq times (sec) DatasetMachinePLINK 1.07PLINK 1.90Ratiosynth1Mac-27.30.2430Mac-126.20.1834Linux32-213.10.5623Linux32-84.30.1824Linux64-5125.40.1827Win32-214.30.6821Win64-29.60.3329synth2Mac-243.30.8452Mac-1238.20.34110Linux32-280.11.942Linux32-825.20.5348Linux64-51234.10.4085Win32-283.61.364Win64-270.80.55130chr1snpMac-252.53.515Mac-1240.51.331Linux32-272.910.27.15Linux32-829.71.421Linux64-51236.81.426Win32-2104.34.523Win64-276.82.235chr1Mac-2403.935.011.5Mac-12163.95.331Linux32-2nomem65.3Linux32-8134.112.810.5Linux64-512144.75.427Win32-2389.221.418.2Win64-2285.38.135This command reports allele frequencies for each variant. The computation is trivial, so the timings just reflect program initialization speed and file I/O efficiency.
