Fig. 2.

Extension possibilities for building alignments. Extension may generally be joint (J), left marginal (L) or right marginal (R). Top: an existing joint alignment may use any type of extension. Grey circles indicate the previously existing alignment, with the new residues added in red, and open circles for when no residue is aligned. Transitioning from joint to marginal alignment sets an endpoint of the alignment. Center: an alignment that is already marginal may only continue with marginal extension on the same side. Bottom: a new alignment may be started in any of the three modes. The joint alignment here is shown skipping a portion of the subtree, but that need not be the case. Initiating an alignment in marginal mode also sets one of the alignment endpoints.