Table 2 Average alignment SP-error, tree error, and TC score across most full-length datasets
Method | ROSE | RNASim | Indelible | ROSE | CRW | 10 AA | HomFam | HomFam |
|---|---|---|---|---|---|---|---|---|
NT | 10K | 10K | AA | (17) | (2) | |||
Average alignment SP-error | ||||||||
UPP | 7.8 (1) | 9.5 (1) | 1.7 (2) | 2.9 (1) | 12.5 (1) | 24.2 (1) | 23.3 (1) | 20.8 (2) |
PASTA | 7.8 (1) | 15.0 (2) | 0.4 (1) | 3.1 (1) | 12.8 (1) | 24.0 (1) | 22.5 (1) | 17.3 (1) |
MAFFT | 20.6 (2) | 25.5 (3) | 41.4 (3) | 4.9 (2) | 28.3 (2) | 23.5 (1) | 25.3 (2) | 20.7 (2) |
Muscle | 20.6 (2) | 64.7 (5) | 62.4 (4) | 5.5 (3) | 30.7 (3) | 30.2 (2) | 48.1 (4) | X |
Clustal | 49.2 (3) | 35.3 (4) | X | 6.5 (4) | 43.3 (4) | 24.3 (1) | 27.7 (3) | 29.4 (3) |
Average ΔFN error | ||||||||
UPP | 1.3 (1) | 0.8 (1) | 0.3 (1) | 1.8 (1) | 7.8 (2) | 3.4 (2) | NA | NA |
PASTA | 1.3 (1) | 0.4 (1) | <0.1 (1) | 1.3 (1) | 5.1 (1) | 3.3 (1) | NA | NA |
MAFFT | 5.8 (2) | 3.5 (2) | 24.8 (3) | 4.5 (3) | 10.1 (3) | 2.3 (1) | NA | NA |
Muscle | 8.4 (3) | 7.3 (3) | 32.5 (4) | 3.1 (2) | 5.5 (1) | 12.6 (3) | NA | NA |
Clustal | 24.3 (4) | 10.4 (4) | X | 4.2 (3) | 34.1 (4) | 3.5 (2) | NA | NA |
Average TC score | ||||||||
UPP | 37.8 (1) | 0.5 (2) | 11.0 (3) | 2.6 (2) | 1.4 (1) | 11.4 (1) | 47.3 (1) | 40.3 (3) |
PASTA | 37.8 (1) | 2.3 (1) | 48.0 (1) | 5.4 (1) | 2.3 (1) | 12.1 (1) | 46.1 (2) | 50.0 (1) |
MAFFT | 31.4 (2) | 0.4 (2) | 7.8 (4) | 0.6 (3) | 0.7 (2) | 12.1 (1) | 45.5 (2) | 46.9 (2) |
Muscle | 9.8 (3) | <0.0 (2) | 18.3 (2) | 2.7 (2) | 0.7 (2) | 10.5 (2) | 27.7 (4) | X |
Clustal | 5.7 (4) | 0.2 (2) | X | 3.1 (2) | 0.1 (2) | 11.8 (1) | 38.6 (3) | 31.0 (4) |