A lot of RNA sequence information is being accumulated and it has become important to add meaning to this. Clustering the RNA sequences helps in finding the function it performs. Paralogus and orthologus genes can also be identified utilizing clustering of RNA sequences.
Miladi M. (2017) et. al. in their recent article have devised a new approach for clustering RNA sequences. This techniques is an advancement to the earlier approaches which do not account for the compensatory base pair Changes. Their technique takes into account the minimum free energy for each structure.
The software is available at http://www.bioinf.uni-freiburg.de/Software/RNAscClust
Reference:
Miladi M. et.al.(2017) RNAscClust: Clustering RNA sequences using structure conservation and graph based motifs.Bioinformatics 33(14):2089-2096.