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Table 7 Performance of aligners on the BAliBASE benchmark database

From: Comprehensive comparison of graph based multiple protein sequence alignment strategies

 

SP

Aligner

RV11 (38)

RV12 (44)

RV20 (41)

RV30 (30)

RV40(49)

RV50 (16)

Overall (218)

MMSA

0.642

0.929

0.918

0.839

0.911

0.895

0.856

ProbCons

0.670

0.941

0.917

0.845

0.903

0.894

0.862

T-Coffee

0.656

0.939

0.914

0.837

0.893

0.895

0.856

MUSCLE

0.572

0.915

0.889

0.814

0.865

0.835

0.815

MAFFT

0.662

0.935

0.927

0.868

0.926

0.903

0.870

ClustalW

0.501

0.865

0.852

0.725

0.789

0.742

0.746

ClustalO

0.590

0.906

0.902

0.862

0.902

0.862

0.837

Kalign

0.605

0.912

0.900

0.813

0.884

0.820

0.822

MSAProbs

0.682

0.946

0.928

0.865

0.925

0.908

0.876

 

Time(sec)

Aligner

RV11 (38)

RV12 (44)

RV20 (41)

RV30 (30)

RV40(49)

RV50 (16)

Overall (218)

MMSA

0.817

1.772

69.797

119.424

38.725

38.453

44.831

ProbCons

2.481

7.052

142.641

297.473

108.307

124.235

113.698

T-Coffee

15.058

23.310

259.227

646.212

202.948

210.856

226.269

MUSCLE

0.701

0.824

5.490

7.538

9.519

7.002

5.179

MAFFT

0.840

1.580

14.071

25.811

27.455

18.434

14.698

ClustalW

0.310

0.923

13.281

25.231

8.155

8.982

9.480

ClustalO

0.406

0.747

4.224

4.824

5.214

4.790

3.368

Kalign

0.054

0.090

0.435

0.562

0.559

0.411

0.352

MSAProbs

2.092

6.436

141.371

295.506

86.463

102.198

105.678

  1. The values in the upper table show the average sum-of-pairs (SP) score and the values in the lower table mean run time achieved by different aligners for each of the six BAliBASE references. The number of alignments in each reference is given in parentheses. Overall values for the entire database are reported in the last column. The best results in each column are shown in bold