SCARNA, pairwise alignment
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Murlet, multiple alignment
C++ source code

MXSCARNA, multiple alignment
C++ source code

RNAmine, structural motif extraction
Software is distributed by direct contact to the author. contact

PHMMTS, sequence-structure alignment
C++ source code

PSTAG, sequence-structure alignment, allow pseudoknots
C++ source code

SOKOS/CAN, marginalized kernel on SCFG
C source code

Stem Kernel
C++ source code

miRRim, miRNA finder
source code

McCaskill-MEA, consensus secondary structure prediction
C++ source code

Rfold, local base pairing probabilities
C++ source code