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Table 2 Comparison of multiple sequence alignment methods

From: MSARC: Multiple sequence alignment by residue clustering

 

SP/TC scores

Computation

Aligner

All

RV11

RV12

RV20

RV30

RV40

RV50

BB40037

Time

Non-progressive methods

      

MSARC

87.6 57.1

69 . 9 46 . 3

94.5 85.7

92.5 39.2

83.7 47.2

93 . 2 62.3

88.7 51.6

98 . 7 70 . 0

16:36:37

DIALIGN-T

77.3 42.8

49.3 25.3

88.8 72.5

86.3 29.2

74.7 34.9

82.0 45.2

80.1 44.2

52.6 0.0

1:13:21

FSA

78.5 42.1

50.3 26.9

92.4 81.8

86.7 18.7

70.7 27.6

85.5 46.2

78.2 39.8

81.8 30.0

35:15:34

PicXAA

87 . 8 59.4

69.0 46 . 3

94.6 86.2

92.5 41.6

86.0 59.8

93.1 62 . 4

89.2 53.0

98 . 7 70 . 0

5:54:18

Progressive methods

      

CLUSTAL Ω

84.0 55.4

59.0 35.8

90.6 78.9

90.2 45.0

86.2 57.5

90.2 57.9

86.2 53.3

61.2 0.0

1 2:1 5

DIALIGN-TX

78.8 44.3

51.5 26.5

89.2 75.2

87.9 30.5

76.2 38.5

83.6 44.8

82.3 46.6

52.8 0.0

1:36:05

MAFFT

86.7 58.4

65.3 42.8

93.6 83.8

92.5 44.6

85.9 58.1

91.5 59.0

90.1 59.4

56.4 0.0

54:04

MSAProbs

87 . 8 60 . 7

68.2 44.1

94 . 6 86 . 5

92 . 8 46 . 4

86 . 5 60 . 7

92.5 62.2

90 . 8 60 . 8

59.5 0.0

6:43:51

MUSCLE

81.9 47.5

57.2 31.8

91.5 80.4

88.9 35.0

81.4 40.9

86.5 45.0

83.5 45.9

48.4 0.0

23:32

Probalign

87.6 58.9

69.5 45.3

94 . 6 86.2

92.6 43.9

85.3 56.6

92.2 60.3

88.7 54.9

54.2 0.0

4:31:41

ProbCons

86.4 55.8

67.0 41.7

94.1 85.5

91.7 40.6

84.5 54.4

90.3 53.2

89.4 57.3

59.3 0.0

6:56:32

T-Coffee

85.7 55.1

65.5 40.9

93.9 84.8

91.4 40.1

83.7 49.0

89.2 54.5

89.4 58.5

50.9 0.0

13:53:02

  1. Columns 2-9 show the mean SP and TC scores for each alignment algorithm on the whole BAliBASE 3.0 dataset, each of its series and case BB40037. The last column presents total CPU computation time (hh:mm:ss). All scores are multiplied by 100. Best results in each column are shown in bold.