Vienna RNA Package中包含了多个用于RNA二级结构预测和比对的程序，以下是官方文档中列出的比对工具：
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 |
相关文献：
Ivo L. Hofacker. Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429-3431 (2003)
软件下载地址：http://www.tbi.univie.ac.at/RNA/