Gardenia – RNA structure alignment
gardenia is a software for RNA structure alignment, based on our ideas presented in Section 3.3 on arc-annotated sequence models. It is enriched with an evolutionary model taking into account affine gap penalties, constraints coming from the primary structure, fast alignment for similar sequences, and local search. It also proposes options for pairwise alignment with tree edit distance, alignment of trees and multiple sequence alignment based on the ClustalW-like progressive alignment strategy. It comes with the RIBOSUM score matrices. It is written in C and is distributed under the GPL license.