RNA

Software

caRNAc - RNA secondary structure inference for set of homologous sequences
caRNAsta - Comparative Analysis of RNA structures by Tree Alignment
cove - COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
ModView - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
NCRNASCAN - a structural RNA genefinder
PHASE - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
PKNOTS - RNA pseudoknot prediction
RNA GENiE - A web based program for the prediction of rna genes in genomic DNA sequences
RNABOB - RNABOB -- fast RNA motif/pattern searcher
RnaViz - a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings
tRNAscan-SE - tRNA detection in genome sequences, detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
Vienna RNA Package - RNA Secondary Structure Prediction and Comparison