Keywords: manual

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## Local versus global alignment

The Kruskal and Sankoff version of the local alignment is implemented [Sankoff & Kruskal, 1983]; this is very similar to the [Smith & Waterman, 1981] method. All the routines for the local alignment are exactly the same as the routines for the global alignment except that during the construction of matrix the alignment is restarted each time the score becomes higher than a cutoff. The second difference is that the backtracking starts from the lowest element in the matrix, wherever it is.