A book reference for visualization of alignment path:
- Gusfield, D. (1997). Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press.

University of Michigan - Ann Arbor

To better use the edit distance algorithm to generate an alignment, we can visualize the alignment as a path through a table, here referred to as the edit distance matrix. The tabular approach of creating a matrix is very helpful to deal with long strings. To compute the alignment path, first, we apply the minimum edit distance algorithm to each cell and store backpointers. Second, we perform a backtrace that starts from the last cell (at the final row and column) and follows the backpointers back to the first cell through the matrix. There might be multiple paths. Each complete path between the final cell and the first cell is a minimum distance alignment.

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