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Table 5 The performance of AMPS on the Master data set with 1987 defaults (PAM250, open gap-penalty 8, single order) and optimised (BLOSUM75, gap-penalty 10, tree order) parameters. Percentage SCR is the percentage of residues in the structurally conserved regions. Acc SCR : accuracy of alignment in SCRs. p : Wilcoxon Signed Rank test probability

From: OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy

PID Average 1

Number of Families 2

Percentage SCR 3

Acc SCR (PAM250/8) 4

Acc SCR (BLOSUM75/10) 5

Difference (5–4)

P

0–10

21

40.5

18.3

22.2

3.9

0.0571

10–20

57

45.4

55.9

60.2

4.3

0.0427

20–30

64

54.1

76.1

81.3

5.2

0.00214

30–50

175

68.6

91.3

92.3

1.0

0.00404

50–100

355

87.8

98.8

98.9

0.1

0.000196

Total

672

74.5

88.5

89.9

1.4

7.4e-09