Table 2. Available programs for secondary structure prediction including pseudoknots.

Program name	Website
HotKnots [47]	http://www.cs.ubc.ca/labs/beta/Software/HotKnots/
hxmatch [46]	http://www.tbi.univie.ac.at/papers/SUPPLEMENTS/HXMATCH/
ILM [48]	http://cs.utsa.edu/~jruan/Software.html
KineFold [26]	http://kinefold.curie.fr/
pknotsRG [29]	http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/
SimulFold [44]	http://people.cs.ubc.ca/~irmtraud/simulfold/
vsfold5 [27]	http://www.rna.it-chiba.ac.jp/~vsfold/vsfold5/

This table provides a list of programs that are available for free and can make predictions on a desktop computer for sequences that are up to at least 200 nucleotides long. Note that hxmatch is designed to find conserved structures for sequences in a multiple alignment and that ILM can be run with one sequence or with an alignment of multiple sequences. SimulFold works on a set of homologous sequences and infers the sequence alignment. KineFold and vsfold5 are available as web servers. pknotsRG is available for use on a web server or for download.