I am trying to align many miRNAs from a variety species, and then auotomatically get miRNA clustering information. MUSCLE or CLUSALW can do alignment (I guess these two tools can align short sequences), but how to get clustering information (e.g., group1 contains miR-1 of species 1 and miR-10 of species2; group2 contains miR-20 of species 1 and miR-13 of species 3)?
I should note only relying on nomenclature at miRBase for miR grouping is not accurate, so sequence alignmnet is needed.
Any of your comments or answers will be helpful for me. THANKS!