Vienna RNA：RNA二级结构预测与比对软件

RNAfold

predict minimum energy secondary structures and pair probabilities

RNAeval

evaluate energy of RNA secondary structures

RNAheat

calculate the specific heat (melting curve) of an RNA sequence

RNAinverse

inverse fold (design) sequences with predefined structure

RNAdistance

compare secondary structures

RNApdist

compare base pair probabilities

RNAsubopt

complete suboptimal folding

RNAplot

RNA structure drawings in PostScript, SVG, or GML

RNAcofold

predict hybrid structure of two sequences

RNAduplex

predict possible hybridization sites between two sequences

RNAup

predict RNA-RNA interaction sites using accessibilities

RNAalifold

predict the consensus structure of several aligned sequences

RNAaliduplex

comparative (multiple alignment) version of RNAduplex

RNALfold

predict locally stable structure of long sequences

RNAplfold

compute average pair probabilities for local base pairs in long sequences

RNApaln

fast structural alignment of RNA sequences using string alignments