Example parse trees. Parse trees are shown for the three sequences/structures from Figure 1, given the CM in Figure 3. For each sequence, each residue must be associated with a state in the parse tree. (The sequences can be read off its parse tree by starting at the upper left and reading counterclockwise around the edge of parse tree.) Each parse tree corresponds directly to a secondary structure – base pairs are pairs of residues aligned to MP states. A collection of parse trees also corresponds to a multiple alignment, by aligning residues that are associated with the same state – for example, all three trees have a residue aligned to state ML4, so these three residues would be aligned together. Insertions and deletions relative to the consensus use nonconsensus states, shown in gray.