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Table 3 Performances of haplotyping programs on simulated data based on some selected genotypes from the 30 European mothers on X-chromosome from the HapMap data.

From: Empirical vs Bayesian approach for estimating haplotypes from genotypes of unrelated individuals

#SNP Sample size Similarity Index Prediction Rate Average Running Time (in seconds)
   Empirical Bayesian Empirical Bayesian Empirical Bayesian
   PL-EM HPlus PHASE HAPLO+ PL-EM HPlus PHASE HAPLO+ PL-EM HPlus PHASE HAPLO+
13 30* 0.783 0.776 0.822 0.683 0.767 0.767 0.800 0.633     
  100 0.969 0.972 0.985 0.979 0.966 0.970 0.977 0.978 0.64 0.16 53.26 2.61
  150 0.981 0.982 0.989 0.981 0.973 0.978 0.989 0.980 0.69 0.23 88.57 2.64
  200 0.986 0.987 0.993 0.984 0.985 0.986 0.992 0.982 0.86 0.30 114.88 5.25
  250 0.988 0.989 0.994 0.979 0.986 0.987 0.992 0.977 0.92 0.38 157.55 6.45
  300 0.927 0.992 0.996 0.984 0.991 0.992 0.992 0.982 0.89 0.40 194.63 7.77
16 30* 0.774 0.807 0.904 0.733 0.700 0.733 0.800 0.667     
  100 0.931 0.933 0.945 0.930 0.897 0.901 0.893 0.905 3.38 1.34 108.74 3.31
  150 0.948 0.951 0.958 0.943 0.909 0.913 0.894 0.919 12.02 1.83 180.08 4.78
  200 0.961 0.963 0.967 0.955 0.923 0.926 0.907 0.932 34.81 2.21 249.74 6.06
  250 0.968 0.968 0.970 0.956 0.930 0.931 0.912 0.934 61.47 2.46 332.92 7.27
  300 0.956 0.971 0.972 0.956 0.928 0.928 0.895 0.932 64.17 2.85 421.54 8.67
12 30* 0.554 0.597 0.614 0.600 0.533 0.567 0.567 0.567     
  100 0.908 0.918 0.925 0.913 0.866 0.873 0.859 0.884 1.46 0.36 76.49 3.49
  150 0.940 0.943 0.945 0.933 0.896 0.899 0.862 0.899 1.52 0.49 127.48 5.08
  200 0.956 0.958 0.957 0.938 0.904 0.906 0.880 0.901 1.61 0.55 173.51 6.61
  250 0.964 0.964 0.963 0.944 0.915 0.917 0.897 0.909 1.64 0.69 202.33 8.85
  300 0.971 0.971 0.969 0.948 0.921 0.921 0.893 0.914 1.67 0.75 278.34 10.13
  1. *: Analysis results of the 30 mothers' genotypes on X-chromosome from the HapMap data
  2. +: HAPLO is short for HAPLOTYPER