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 | Â | Â | Â | Â |
 | 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 | Â | Â | Â | Â |
 | 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 | Â | Â | Â | Â |
 | 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 |