Table 4 Accuracy and time comparison of the algorithms on four real datasets involving different numbers of genotypes
From: ISHAPE: new rapid and accurate software for haplotyping
ACE | APOE | GH1 | Chr 5q31 | |||||
|---|---|---|---|---|---|---|---|---|
11 genotypes | 80 genotypes | 153 genotypes | 258 genotypes | |||||
Prog | SER | Time (sec.) | SER | Time (sec.) | SER | Time (sec.) | SER | Time (sec.) |
Ishape1 | 0.0190 +/- 0.002 | 0.8 | 0.055 +/- 0.001 | 0.2 | 0.065 +/- 0.003 | 0.9 | 0.0473 +/- 0.001 | 512 |
Ishape2 | 0.0184 +/- 0.0006 | 4.96 | 0.050 +/- 0.005 | 3.5 | 0.052 +/- 0.004 | 9.2 | 0.0451 +/- 0.001 | 5744 |
Phase1.0 | 0.0186 +/- 0.001 | 4.82 | 0.055 +/- 0.001 | 2.7 | 0.065 +/- 0.004 | 15.6 | 0.0657 +/- 0.002 | 21536 |
Phase2.1 | 0.0175 +/- 0.000 | 23.25 | 0.049 +/- 0.005 | 14 | 0.052 +/- 0.003 | 62.9 | 0.0501 +/- 0.001 | 61789 |
fastPhase | 0.0182 +/- 0.001 | 37.61 | 0.103 +/- 0.009 | 49.1 | 0.056 +/- 0.003 | 139.1 | 0.0452 +/- 0.001 | 986 |
PL-EM | 0.0573 +/- 0.005 | 0.51 | 0.165 +/- 0.000 | 0.11 | 0.060 +/- 0.004 | 0.31 | 0.0601 +/- 0.001 | 6507 |
2snp | 0.0116 +/- 0.000 | <0.1 | 0.230 +/- 0.000 | < 0.1 | 0.074 +/- 0.000 | < 0.1 | 0.0513 +/- 0.000 | 3 |