pAliKiss predicts RNA secondary structures for fixed RNA multiple sequence alignments, with special attention for pseudoknotted structures.

The program pAliKiss is the offspring of the hybridization of RNAalishapes for folding alignments and pKiss for considering canonical simple recursive pseudoknots besides "normal" nested structures.

Author: S. Janssen

Users of pAliKiss are requested to cite :

Janssen, Stefan and Giegerich, Robert The RNA shapes studio, Bioinformatics, 2015