Applying the Smith-Waterman Similarity to Cellular Automata

The Smith–Waterman similarity (SWS) dynamic algorithm aligns two sequences of data (strings or arrays) to determine how well they match. This has been extensively applied in molecular biology to find related DNA nucleotide or protein sequences.
The SWS algorithm is used here to align the two cellular automaton (CA) paths to check for similarities between them. The recurrence plot shows an interesting visual pattern; note that the diagonal lines in red have a 100% match because the same steps align the and dimensions (columns and rows).


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