The Probabilistic Evolutionary and Thermodynamic (PET) model unifies evolutionary and thermodynamic information about RNA secondary structures in one probabilistic model. Based on this model we developed PETfold  and PETcofold [2,3] which predict the consensus RNA secondary structure from an RNA alignment and the joint secondary structure including RNA-RNA interactions from two RNA alignments, respectively.
The web server  offers to both methods a seperate input page on which the user can input or upload sequence alignments, phylogenetic trees, and consensus secondary structures, and specify options. It is also possible to select an Rfam family and/or an human 17way MULTIZ alignment for finding binding sites or predicting their RNA structure. After submission PETfold or PETcofold, respectively, is started on our internal cluster under an unique job identifier. The user will be directly redirected to the result page for fast jobs. Otherwise, the user can access the results everytime using the unique job identifier. The results are presented by figures of the phylogenetic tree, the alignment with barplots of pairing reliabilities and sequence conservation, the consensus RNA secondary structure, and reliability dot plots.
 Seemann SE, Gorodkin J, Backofen R "Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments", Nucleic Acids Res., 36(20):6355-62, 2008.
 Seemann SE, Richter AS, Gorodkin J, Backofen R "Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions", Algorithms Mol Biol., 5:22, 2010.
 Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J "PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences", Bioinformatics, 27(2):211-9, 2011.
 Seemann SE, Menzel P, Backofen R, Gorodkin J "The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.", Nucleic Acid Res., 39(Web Server issue):W107-11, 2011.