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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