A branch-and-cut algorithm for multiple sequence alignment by Althaus E.

By Althaus E.

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For every variable v, we compute an upper bound Uv on the value of the optimal alignment in which variable v takes the value 1, and we can permanently fix the variable to 0 if Uv ≤ L. These upper bounds are determined as follows. First of all, we compute all optimal alignments between two strings s i , s j , for i, j = k i j i j 3 1, . . , k, i < j in O( k−1 j =i+1 |s ||s | max{|s |, |s |}) = O(n ) time by the foli=1 lowing modification of the standard dynamic programming technique for the case in which wa = 0 for a ∈ Ag [15].

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