Table 4.

A Selection of Tools for the Detection of Secondary Structures in RNA Viruses

Tool	Description	Alignment	Ref.
RNAfold	RNAfold is a tool to predict secondary structures of single stranded RNA or DNA sequences.	No	Gruber et al. (2008)
mfold	mfold is a web server that provides easy access to RNA and DNA folding and hybridization software.	No	Zuker (2003)
RNAalifold	RNAalifold is a tool for calculating secondary structures for a set of aligned RNAs. It is part of the Vienna RNA Package.	Yes	Hofacker (2007)
LocARNA	LocARNA is a multiple alignment tool based on the calculation of sequence and structure simultaneously.	Yes	Will et al. (2007)
LRIscan	LRIscan is a tool for the prediction of long-range interactions in full viral genomes based on a multiple genome alignment. LRIscan is able to find interactions spanning thousands of nucleotides.	Yes	Fricke and Marz (2016)