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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