A limited number of RNA comparative structure prediction methods can handle pseudoknots due to the computational complexity. Several of these methods take a sequence alignment as an input. ILM is an algorithm that takes as an input either individual sequences or a sequence alignment (Ruan et al., 2004) . A base pair score matrix is prepared initially and helices are added to the structure in an iterative fashion. In the approach hxmatch, a maximum weighted matching algorithm with combined thermodynamic and covariance scores is used (Witwer et al., 2004) . This program gives the option to be combined with RNAalifold.