From: Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
 | Alignments | Better (count) | Worse (count) | Better (avg. (stdev)) | Worse (avg. (stdev)) |
---|---|---|---|---|---|
High Similarity | model trim vs. optimal | 10 | 0 | 0.018 (0.014) | 0 |
 | robust trim vs. optimal | 8 | 0 | 0.019 (0.014) | 0 |
 | frequency trim vs. optimal | 11 | 0 | 0.015 (0.013) | 0 |
 | local trim vs. optimal | 15 | 0 | 0.024 (0.016) | 0 |
 | local trim + model trim vs. local | 4 | 6 | 0.013 (0.010) | -0.009 (0.003) |
 | model alignment vs. optimal | 8 | 3 | 0.024 (0.031) | -0.008 (0.003) |
 | robust alignment vs. optimal | 3 | 12 | 0.024 (0.013) | -0.170 (0.170) |
 | frequency alignment vs. optimal | 8 | 1 | 0.022 (0.030) | -0.012 |
Medium Similarity | model trim vs. optimal | 14 | 1 | 0.056 (0.058) | -0.009 |
 | robust trim vs. optimal | 14 | 0 | 0.061 (0.056) | 0 |
 | frequency trim vs. optimal | 13 | 1 | 0.053 (0.057) | -0.009 |
 | local trim vs. optimal | 14 | 3 | 0.098 (0.084) | -0.012 (0.005) |
 | local trim + model trim vs. local | 9 | 8 | 0.061 (0.056) | -0.015 (0.009) |
 | model alignment vs. optimal | 10 | 2 | 0.039 (0.043) | -0.020 (0.018) |
 | robust alignment vs. optimal | 2 | 19 | 0.062 (0.000) | -0.250 (0.140) |
 | frequency alignment vs. optimal | 8 | 2 | 0.045 (0.043) | -0.020 (0.018) |
Low Similarity | model trim vs. optimal | 12 | 1 | 0.054 (0.066) | -0.024 |
 | robust trim vs. optimal | 17 | 0 | 0.051 (0.055) | 0 |
 | frequency trim vs. optimal | 12 | 1 | 0.055 (0.066) | -0.024 |
 | local trim vs. optimal | 18 | 2 | 0.110 (0.100) | -0.280 (0.380) |
 | local trim + model trim vs. local | 10 | 3 | 0.041 (0.065) | -0.013 (0.005) |
 | model alignment vs. optimal | 7 | 2 | 0.021 (0.014) | -0.034 (0.022) |
 | robust alignment vs. optimal | 2 | 16 | 0.150 (0.050) | -0.240 (0.170) |
 | frequency alignment vs. optimal | 5 | 3 | 0.022 (0.016) | -0.029 (0.018) |