Dynamic programming table traversal. The multiple alignment prefixes (represented by o symbols) traversed by the one-state recursion, when the input is the homology structure of Fig. 1. (For clarity, the vectors are plotted in two dimensions instead of the actual three.) The homology structure is represented by the graph, and each directed path on this graph uniquely corresponds to an alignment that is compatible with the homology structure.
Lunter et al. BMC Bioinformatics 2005 6:83 doi:10.1186/1471-2105-6-83