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RNAalishapes

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Choose one of RNAalishapes functions ...

probs : computes probabilistic shape analysis.

shapes : computes shape representative structures.

sample : sampling of shape class probabilities via stochastic backtracing.

mfe : computes the single energetically best secondary structure.

subopt : predicts mfe & energetically suboptimal structures.

mea : computes the maximum expected accuracy (MEA) secondary structure.

outside : computes base-pair probabilities.

eval : evaluates the free energy of an RNA molecule in fixed secondary structure.

abstract : abstracts a dot-Bracket string into a shape string.

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