By Althaus E.
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Additional resources for A branch-and-cut algorithm for multiple sequence alignment
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Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Science 89, 10915–10919 (1992) 17. : Using separation algorithms to generate mixed integer model reformulations. Oper. Res. Lett. 10, 119–128 (1991) 18. : Online dynamic programming with applications to the prediction of rna secondary structure. In: Proceedings of the First Symposium on Discrete Algorithms 1990, pp 503–512 19. LEDA (Library of Efficient Data Types and Algorithms), 2004. com 20. : An exact solution for the segment-to-segment multiple sequence alignment problem.
This corresponds to introducing O(n2 ) new variables and constraints. Variable reduction Even for rather small instances, the number of variables in our ILP k i j 2 formulation is very large, namely there are k−1 j =i+1 |s ||s | = O(n ) edge varii=1 ables and ki=1 (k − 1) |s 2|+1 = O(n3 ) arc variables. For example, an instance with 5 strings of length 100 has 201, 000 variables. Most of these variables are very unlikely to take the value 1 in an optimal solution. In this section, we describe a simple but successful method to reduce the number of variables.