Alignment-tools

AltAVist - AltAVist : Alternative Alignment Visualization Tool

ClustalW - general purpose multiple sequence alignment program for DNA or proteins

dca - Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences.

InSilicoDicer - InSilicoDicer - Intrinsic and Extrinsic Prediction of mature miRNA.

Locomotif - Locomotif: Localization of RNA motifs with generated thermodynamic Matchers

paRNAss - paRNAss - Prediction of Alternate RNA Secondary Structures.

planACstar - planACstar is an implementation of plan AC* that improves structural RNA alignments by structure comparison .

RNAforester no description available

RNAhybrid - finding minimum free energy hybridization

RNAsifter -