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Table 1 –freq times (sec)

From: Second-generation PLINK: rising to the challenge of larger and richer datasets

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
  1. 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.