The RNA tools offer a series of bioinformatics program specifically designed for the analysis of structural RNA: secondary structure inference, alignment, annotation.
Carnac
Predicts the consensus secondary structure for a set of homologous, unaligned RNA sequences. Very fast and accurate.
miRkwood
Fast and easy identification of microRNAS in plant genomes. Works with both small RNA sequencing data and full genomic sequences.
Gardenia
Comparison and multiple alignment of RNA sequences. The algorithm takes into account both the primary structure and the secondary structure to build a good alignment.
RNAspace
Annotation platform for noncoding RNAs
Regliss
This tools builds all locally optimal secondary structures of an RNA sequence, which provide a useful insight into the folding landscape of the molecule.
CG-seq
It is a software pipeline to identify noncoding RNA genes in genomic sequences by comparative analysis and multispecies comparison.