Table 2 Alignment and tree accuracy metrics for all methods on 1,000 sequences
From: Scaling statistical multiple sequence alignment to large datasets
| Â | Â | Â | Â | Â | Delta-RF | |
|---|---|---|---|---|---|---|
Data | Method | Prec. | Rec. | TC | RAxML | FT-2 |
Indelible | P(Default) | 95.1 % | 94.6 % | 4.5 % | 1.86 % | 0.68 % |
M2 | P+BAli-Phy | 98.7 % | 98.7 % | 14.6 % | 0.29 % | -0.72 % |
| Â | P+MAFFT-L | 97.2 % | 97.0 % | 6.8 % | 0.75 % | -0.20 % |
| Â | MAFFT-L | 80.2 % | 75.0 % | 1.4 % | 15.73 % | 8.74 % |
| Â | MAFFT-def | 1.0 % | 0.4 % | 0.0 % | (not run) | (not run) |
RNAsim | P(default) | 90.3 % | 90.4 % | 3.5 % | 0.56 % | 0.33 % |
| Â | P+BAli-Phy | 92.1 % | 92.1 % | 8.5 % | 0.70 % | 0.42 % |
| Â | P+MAFFT-L | 88.8 % | 89.0 % | 3.9 % | 0.34 % | 0.45 % |
| Â | MAFFT-L | 91.8 % | 91.5 % | 2.9 % | 0.73 % | 6.47 % |
| Â | MAFFT-def | 83.7 % | 71.5 % | 1.4 % | (not run) | (not run) |
Rose L1 | P(default) | 90.9 % | 90.6 % | 15.9 % | 2.07 % | 2.24 % |
| Â | P+BAli-Phy | 91.8 % | 91.7 % | 33.2 % | 1.47 % | 1.51 % |
| Â | P+MAFFT-L | 90.0 % | 89.8 % | 21.8 % | 1.98 % | 2.00 % |
| Â | MAFFT-L | 84.1 % | 76.6 % | 6.4 % | 3.45 % | 3.15 % |
| Â | MAFFT-def | 1.1 % | 0.4 % | 0.0 % | (not run) | (not run) |
Rose M1 | P(default) | 79.7 % | 79.0 % | 9.0 % | 5.35 % | 6.26 % |
| Â | P+BAli-Phy | 79.8 % | 79.6 % | 24.4 % | 4.70 % | 5.45 % |
| Â | P+MAFFT-L | 78.6 % | 78.2 % | 12.9 % | 5.96 % | 5.89 % |
| Â | MAFFT-L | 74.9 % | 63.3 % | 3.0 % | 3.64 % | 3.90 % |
| Â | MAFFT-def | 1.2 % | 0.5 % | 0.0 % | (not run) | (not run) |
Rose S1 | P(default) | 85.3 % | 85.1 % | 2.8 % | 3.94 % | 4.29 % |
| Â | P+BAli-Phy | 84.3 % | 84.3 % | 10.3 % | 2.26 % | 3.59 % |
| Â | P+MAFFT-L | 83.5 % | 83.3 % | 4.8 % | 3.55 % | 4.38 % |
| Â | MAFFT-L | 76.2 % | 68.2 % | 0.5 % | 3.80 % | 3.79 % |
| Â | MAFFT-def | 1.2 % | 0.5 % | 0.0 % | (not run) | (not run) |