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Table 1 Overview of methods

From: Strategies for measuring evolutionary conservation of RNA secondary structures

Category Methods Description References
Methods based on folding energies SCI RNAalifold consensus energy normalized by dividing by the average energy of the single sequences folded independently. [7]
  SCI RN Aeval Evaluation of energies of sequences under the constraint of being forced to fold into the structures of the other sequences in comparison to the unconstrained energies. this work
Methods based on single structures Base-pair distance Number of base-pairs not shared by two structures. [64]
  Mountain metric Distance as the difference of two mountain functions, which give the number of base-pairs enclosing a position. [40]
  Tree editing Based on the representation of RNA secondary structures as trees. A distance is deined as the cost of transforming one tree into the other. [41-43]
Methods considering the entire folding space Ensemble distance Base-pair distance extended to compare ensembles of structures. this work
  Ensemble mountain metric Distance as the difference of two mountain functions, which give the number of base-pairs that are, on average, expected to enclose a position. [47]
  RNApdist like distance Distance measure based on the comparison of vectors of probabilities of being paired upstream, paired downstream, and unpaired. [33,48]
  RNAshapes Similarity measure based on probabilities of abstract shapes. [49]
Other Methods ddbRNA Evaluates compensatory mutations in all possible stem loops in all sequences of an alignment. [9]
  MSARi Evaluation of the statistical significance of short, contiguous potential base-pair regions under different distribution models. [8]