MARNA is not maintained anymore since 2005. For the task of multiple sequence-structure RNA alignment the more advanced tool LocARNA is superseding MARNA (check fixed structure input in LocARNA help page).
MARNA is a multiple alignment of RNAs taking into consideration both the primary sequence and the secondary structure. It is based on pairwise comparisons using costs of edit operations. The edit operations can be divided into edit operations on arcs and edit operations on bases. Additionally, MARNA predicts a consensus sequence as well as a consensus structure.