A Lua script wrapped around the Crumple program (see, https://www.ncbi.nlm.nih.gov/pubmed/27665589) allowing for generation and filtering of all possible RNA structures in a given sequence, and pairwise comparison between a group of sequences to look for conservation. Resulting conserved structures are plotted in R.
Used in publication:
Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes. https://www.ncbi.nlm.nih.gov/pubmed/28973853 PMID: 28973853 PMC: PMC5642728 DOI: 10.1073/pnas.1714385114