DotKnot-PW was compared with methods that are freely available and use standard input and output formats. The comparative methods are CARNAC, Tfold and hxmatch (with the -A option using RNAalifold). All of these methods return structure predictions for only the reference structure with regards to the support set of evolutionarily related sequences. Tfold and hxmatch take a sequence alignment as the input. ClustalW with the default parameters was used to produce the initial sequence alignment. DotKnot-PW and CARNAC take a set of unaligned sequences as the input. Furthermore, prediction results for the reference sequence (not the supporting sequences) were obtained from the single sequence methods DotKnot (Sperschneider and Datta, 2010; Sperschneider et al., 2011), ProbKnot (Bellaousov and Mathews, 2010) , IPknot (Sato et al., 2011) and RNAfold (Hofacker et al., 1994) . Note that all methods except CARNAC and RNAfold allow pseudoknot prediction.