Figure 3.

Crossovers between two alignments containing no interchange columns.a) Two alignments coded under the map C, as described in Equation (1). b) The resulting alignment DAG allows for crossovers between these alignments, such that there are four possible paths through the DAG, two of which include pairs of columns that are not observed in the input alignments (dashed lines). c) Correspondence between alignment columns and edges connecting cells in a dynamic programming matrix.