From: Strategies for measuring evolutionary conservation of RNA secondary structures
 |  | Structural | CLUSTAL W | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Method | Variant | Low | Medium | High | Low | Medium | High | ||||||
Energy based | SCI | 0.79 | 0.32 | 0.95 | 0.70 | 1.00 | 1.00 | 0.79 | 0.31 | 0.80 | 0.42 | 0.90 | 0.72 |
 | RNAeval | 0.82 | 0.43 | 0.86 | 0.45 | 1.00 | 0.99 | 0.82 | 0.42 | 0.76 | 0.32 | 0.90 | 0.68 |
Base-pair distance | consensus | 0.80 | 0.28 | 0.93 | 0.56 | 1.00 | 0.99 | 0.79 | 0.27 | 0.85 | 0.40 | 0.92 | 0.79 |
 | pairwise | 0.83 | 0.28 | 0.90 | 0.54 | 0.99 | 0.98 | 0.83 | 0.27 | 0.81 | 0.40 | 0.90 | 0.78 |
Mountain metric | consensus | 0.78 | 0.34 | 0.82 | 0.38 | 0.92 | 0.63 | 0.78 | 0.34 | 0.73 | 0.29 | 0.80 | 0.41 |
 | pairwise | 0.79 | 0.29 | 0.75 | 0.33 | 0.76 | 0.34 | 0.79 | 0.29 | 0.73 | 0.30 | 0.75 | 0.34 |
Tree editing | consensus, full | 0.77 | 0.32 | 0.88 | 0.44 | 0.99 | 0.95 | 0.77 | 0.32 | 0.77 | 0.31 | 0.86 | 0.60 |
 | consensus, HIT | 0.76 | 0.30 | 0.89 | 0.46 | 0.99 | 0.97 | 0.76 | 0.28 | 0.78 | 0.33 | 0.87 | 0.60 |
 | consensus, coarse grained | 0.71 | 0.22 | 0.81 | 0.34 | 0.95 | 0.73 | 0.72 | 0.21 | 0.74 | 0.26 | 0.83 | 0.45 |
 | consensus, w. coarse grained | 0.74 | 0.26 | 0.84 | 0.36 | 0.98 | 0.88 | 0.74 | 0.25 | 0.73 | 0.28 | 0.82 | 0.46 |
 | pairwise, full | 0.78 | 0.31 | 0.77 | 0.36 | 0.88 | 0.63 | 0.78 | 0.31 | 0.75 | 0.34 | 0.87 | 0.56 |
 | pairwise, HIT | 0.77 | 0.27 | 0.77 | 0.36 | 0.90 | 0.66 | 0.76 | 0.26 | 0.76 | 0.34 | 0.89 | 0.63 |
 | pairwise, coarse grained | 0.72 | 0.16 | 0.68 | 0.23 | 0.74 | 0.24 | 0.72 | 0.16 | 0.68 | 0.22 | 0.78 | 0.30 |
 | pairwise, w. coarse grained | 0.76 | 0.23 | 0.71 | 0.28 | 0.81 | 0.41 | 0.75 | 0.15 | 0.71 | 0.23 | 0.82 | 0.35 |
 | pairwise, MiGaL-Layer 0 | 0.62 | 0.07 | 0.61 | 0.07 | 0.67 | 0.06 | 0.62 | 0.07 | 0.60 | 0.06 | 0.66 | 0.04 |
 | pairwise, MiGaL-Layer 1 | 0.74 | 0.27 | 0.68 | 0.24 | 0.77 | 0.33 | 0.74 | 0.27 | 0.68 | 0.24 | 0.76 | 0.33 |
 | pairwise, MiGaL-Layer 2 | 0.74 | 0.23 | 0.70 | 0.29 | 0.82 | 0.42 | 0.73 | 0.22 | 0.69 | 0.27 | 0.78 | 0.37 |
 | pairwise, MiGaL-Layer 3 | 0.76 | 0.27 | 0.71 | 0.30 | 0.84 | 0.49 | 0.75 | 0.26 | 0.71 | 0.29 | 0.82 | 0.47 |
Ensemble distance | consensus | 0.64 | 0.32 | 0.61 | 0.15 | 0.72 | 0.25 | 0.63 | 0.31 | 0.60 | 0.14 | 0.70 | 0.24 |
 | pairwise | 0.65 | 0.42 | 0.61 | 0.15 | 0.72 | 0.26 | 0.65 | 0.32 | 0.61 | 0.30 | 0.72 | 0.31 |
Mountain metric using base-pair probabilities | consensus | 0.48 | 0.17 | 0.58 | 0.27 | 0.65 | 0.40 | 0.50 | 0.18 | 0.56 | 0.24 | 0.61 | 0.28 |
 | pairwise | 0.78 | 0.32 | 0.75 | 0.34 | 0.76 | 0.31 | 0.79 | 0.32 | 0.72 | 0.30 | 0.74 | 0.31 |
RNApdist-like | consensus | 0.76 | 0.28 | 0.79 | 0.37 | 0.89 | 0.44 | 0.76 | 0.27 | 0.73 | 0.30 | 0.74 | 0.25 |
 | pairwise | 0.75 | 0.25 | 0.78 | 0.36 | 0.86 | 0.45 | 0.75 | 0.24 | 0.73 | 0.28 | 0.78 | 0.30 |