PSMAlign is an open source tool that performs pairwise RNA secondary structures alignment based on the conserved stem pattern discovered. It enables alignment of large structures, such as those in the 23S ribosomal RNA family. Arbitrary pseudoknots are also allowed.
Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen
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Pairwise RNA secondary structure alignment with conserved stem pattern.
Chiu JK, Chen YP.
Bioinformatics. 2015 Aug 13. pii: btv471.