Fig. 3.

Extension possibilities at bifurcations. A bifurcation state joins two subtrees, one 5′ (left, blue) and one 3′ (right, red). Each subtree has its own alignment mode, either joint (J), left marginal (L), right marginal (R), or empty (∅). The subtree modes together must give a continuous subsequence, and all valid combinations are shown. The combination determines the mode of the bifurcation state, which can subsequently be extended like any other state, except for the terminal case T. (Arrows show possibilities for later extension.)