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pAliKiss
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Choose one of pAliKiss functions ...
mfe : computes the single energetically best secondary structure.
subopt : predicts mfe & energetically suboptimal structures.
enforce : predicts mfe, assuming input alignment has to fold into a pseuoknot.
local : predicts local mfe & suboptimal pseudoknots, i.e. leading and trailing alignment columns can be omitted.
shapes : computes abstract shape analysis.
probs : computes probabilistic shape analysis.
eval : evaluates the free energy of a fixed RNA multiple sequence alignment for a fixed secondary structure.
abstract : abstracts a dot-Bracket string into a shape string.
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