The structural alignment is converted to a guide tree. Left: the consensus secondary structure is derived from the annotated alignment in Figure 1. Numbers in the circles indicate alignment column coordinates: e.g. column 4 base pairs with column 14, and so on. Right: the CM guide tree corresponding to this consensus structure. The nodes of the tree are numbered 1..24 in preorder traversal (see text). MATP, MATL, and MATR nodes are associated with the columns they generate: e.g., node 6 is a MATP (pair) node that is associated with the base-paired columns 4 and 14.