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The effectiveness of calculating suboptimal alignments using different methods
| The method of alignment calculation | % Alignments significantly improved | Average number of alignments | Maximum number of alignments | Minimum number of alignments |
| Parametric method | 34 | 49 (34) | 138 | 1 |
| Iterative method | 35 | 275 (130) | 469 | 25 |
| Hybrid method | 48 | 733 (300) | 2210 | 131 |
Only the results for the moderate similarity range (FFAS z-score 14–7) are shown. Values of variance are given in parentheses.
