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Table 4 The numbers in the upper diagonal refer to the combined execution time for total HSP calculation, hit sorting and all-vs-all comparison of both strands (forward and reverse) in seconds (acronyms as described in Table 3). The charts in the bottom part are symmetric visual representations of the corresponding cell in the upper diagonal (bar colour legend: blue =GECKO; orange =Gepard; grey =Lastz; and yellow =MUMmer). The total execution time (in seconds) for all the comparisons were: GECKO - 318591, Gepard - 576889, Lastz - 4752315 and MUMmer - 558360. The total time for GECKO represents a dummy execution, the actual execution time (executing the dictionary calculation once) was of 142954

From: Breaking the computational barriers of pairwise genome comparison

 

Method

HS

PT

MM

PA

GG

MMU

RN

BT

CF

SS

HS

GECKO

 

19190

2438

11282

11433

9358

11367

3768

2944

5875

 

Gepard

 

6152

2581

12973

2861

8644

11478

5850

5540

14880

 

Lastz

 

158874

140255

117398

105912

108312

96593

63294

70904

157619

 

MUMmer

 

13891

2536

7519

11083

31164

10566

2127

3277

10170

PT

GECKO

 

2932

10567

9287

9686

10800

3766

2939

5909

 

Gepard

  

15662

22242

26400

27394

9113

11362

10445

12856

 

Lastz

  

135093

191012

181386

210949

164312

171510

146315

115160

 

MUMmer

  

6214

23434

43301

27051

9640

1594

2836

10384

MM

GECKO

 

3322

5432

5306

7558

4461

3294

6387

 

Gepard

   

16356

16675

15573

9349

8663

7111

13517

 

Lastz

   

141032

128324

136632

128874

72552

57393

133667

 

MUMmer

   

4512

6669

17013

25387

1736

6005

10423

PA

GECKO

 

31137

10012

5907

3770

3081

5879

 

Gepard

    

28282

25929

11305

11727

11680

14778

 

Lastz

    

148768

167206

135357

82444

63000

157305

 

MUMmer

    

15115

36458

19321

3330

3170

11564

GG

GECKO

 

9703

5957

5206

5294

7895

 

Gepard

     

25819

9960

13355

13250

13244

 

Lastz

     

137351

63414

44411

28089

66732

 

MUMmer

     

36614

11729

6869

30429

45431

MMU

GECKO

 

5908

5159

5170

5873

 

Gepard

      

10229

12219

11360

13493

 

Lastz

      

58823

44641

32046

92761

 

MUMmer

      

8546

1307

2756

10128

RN

GECKO

 

5930

5894

5935

 

Gepard

       

8143

6458

17278

 

Lastz

       

47869

39163

79895

 

MUMmer

       

1979

4702

15277

BT

GECKO

 

3777

5914

 

Gepard

        

6574

9827

 

Lastz

        

21861

56029

 

MUMmer

        

717

1608

CF

GECKO

 

5889

 

Gepard

         

8302

 

Lastz

         

51778

 

MUMmer

         

2777

SS

GECKO

 
 

Gepard

          
 

Lastz

          
 

MUMmer