Overview of WSD. WSD constructs a DP matrix similar to sequence alignment (with mismatch and gap penalties set to 1 in this example). Each cell in the matrix represents the minimum decomposition cost at that position. The purple arrows indicate the decomposition path, analogous to an alignment path, which determines the final decomposition result. Blue-labeled DP cells represent “template-transition” cells, allowing the decomposition path to jump between specific DP cells of different templates. The WSD output is a TSV file with columns: TR name/TR start/TR end/alignment direction (“+” for forward, “−” for reverse complement)/template name/identity score.