An O(n log log n) time O(n) space algorithm for anchored edit distance chaining is obtained by merging gap-cost computation from Chao and Miller (1995) with overlap-cost computation from Baker and Giancarlo (1998), plus a practical O(n log n) implementation.
33 Filip Pavetić, Ivan Katanić, Gustav Matula, Goran Žužić, and Mile Šikić
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Revisiting $O(n \log \log n)$ chaining for anchored edit distance
An O(n log log n) time O(n) space algorithm for anchored edit distance chaining is obtained by merging gap-cost computation from Chao and Miller (1995) with overlap-cost computation from Baker and Giancarlo (1998), plus a practical O(n log n) implementation.