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By Althaus E.

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Vm l = m + 1, to denote the set of arcs that span either i or v i vm m+1 collection of all maximal pairwise-incompatible sets of j edges S ⊆ E ij such that, for each edge {vli , vm } ∈ S, lb ≤ l ≤ le and mb ≤ m ≤ me Acknowledgements. We are grateful to an anonymous referee for the very detailed and helpful report and Tobias Achterberg for his patience in explaining us the details of this branch-and-cut framework SCIP. This work was partially supported by a fellowship within the ICSI Postdoc Program of the German Academic Exchange Service (DAAD), and by the German Federal Ministry of Education and Research, grant no.

Html 28. : On the complexity of multiple sequence alignment. J. Comput. Biol.

4. Computational experiments We tested our implementation, called COSA (COmbinatorial SequenceAlignment) using instances of the BAliBase library [27], containing 4 to 6 strings of about 50-130 amino acids each, subdivided into three groups according to different “identity levels”, that represent an index of the similarity of the strings (Group V1: identity > 35%, Group V2: identity 20 − 40%, Group V3: identity < 25%). The library also offers an evaluation program that computes a score between 0 and 1 indicating the percentage of correctly aligned characters with respect to reference alignments that have been hand-created using structural information.

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

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