A branch-and-cut algorithm for multiple sequence alignment

@article{Althaus2006ABA,
  title={A branch-and-cut algorithm for multiple sequence alignment},
  author={Ernst Althaus and Alberto Caprara and Hans-Peter Lenhof and Knut Reinert},
  journal={Mathematical Programming},
  year={2006},
  volume={105},
  pages={387-425}
}
We consider a branch-and-cut approach for solving the multiple sequence alignment problem, which is a central problem in computational biology. We propose a general model for this problem in which arbitrary gap costs are allowed. An interesting aspect of our approach is that the three (exponentially large) classes of natural valid inequalities that we consider turn out to be both facet-defining for the convex hull of integer solutions and separable in polynomial time. Both the proofs that these… Expand
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