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Table 3 Accuracy and time comparison of the algorithms on the HapMap data.

From: ISHAPE: new rapid and accurate software for haplotyping

 

Contiguous SNPs

Spaced by 5 kb

Software

Average

SER (%)

Median

SER (%)

Average

ranking

Average

time (sec)

Average

SER (%)

Median

SER (%)

Average

ranking

Average

time (sec)

FastPhase

1.31 +/- 0.16

0.68

2.81 +/- 0.14

100.4

3.98 +/- 0.30

2.99

2.79 +/- 0.12

88.8

Ishape1

1.40 +/- 0.16

0.63

2.87 +/- 0.15

5.0

4.88 +/- 0.36

3.51

3.99 +/- 0.15

12.3

Ishape2

1.10 +/- 0.14

0.51

1.89 +/- 0.10

34.9

3.60 +/- 0.29

2.48

2.01 +/- 0.09

66.1

Phase1.0

1.39 +/- 0.16

0.68

2.80 +/- 0.15

52.2

4.92 +/- 0.36

3.53

4.04 +/- 0.15

142.5

Phase2.1

1.17 +/- 0.14

0.58

2.21 +/- 0.13

215.0

3.57 +/- 0.27

2.53

2.11 +/- 0.10

702.0

PL-EM

1.81 +/- 0.22

0.85

3.87 +/- 0.18

6.7

5.88 +/- 0.42

4.27

5.02 +/- 0.16

5.8

2snp

1.77 +/- 0.15

1.20

4.31 +/- 0.19

0.1

4.71 +/- 0.28

4.01

4.24 +/- 0.17

0.1

  1. Different size of SNP datasets are tested under two assumptions for the choice of the SNPs retained: adjacent SNPs and SNPs spaced by 5 kb in average. All the SNPs have a MAF above 1%. For each given size 10, 20, 30, 40, 50, 60, and 80 SNPs, one hundred different SNPs datasets were tested. The Table provides a summary showing the average performances obtained over entire HAPMAP segments tested. The 3rd column presents the average rank i.e. the mean of the ranks given to each software regarding the SER they obtained for each experiment. The last column gives the average time obtained for the experiments. 95% confidence intervals are provided for the SER and for the ranking (total of 700 experiments). Best performances are highlighted in bold.
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BMC Bioinformatics

ISSN: 1471-2105

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