The new Semi-Automated RNA Sequence Editor SARSE might also be of interest.
FOLDALIGN an algorithm for local or global simultaneous folding and aligning
two or more RNA sequences and is based on the Sankoffs algorithm (SIAM J. Appl.
Math., 45:810-825, 1985). Foldalign can make pairwise local or global
alignments and structure predictions. FoldalignM makes a multiple global
alignment and structure prediction.