Divide-and-conquer multiple alignment with segment-based constraints

A large number of methods for multiple sequence alignment are currenty available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. Global</it> strategies can be outperformed by approaches based on local</it> similarities and vice versa, depending on the characteristics of the input sequences. In recent years, mixed</it> approaches that include both global and local features have shown promising results. Herein, we introduce a new algorithm for multiple sequence alignment that integrates the global divide-and-conquer</it> approach with the local segment-based</it> approach, thereby combining the strengths of those two strategies. Contact: <inter-ref locator="micha@sammeth.net"locator-type="email">micha@sammeth.net</inter-ref> <fn id="fn0"><no>*</no> To whom correspondence should be addressed. </fn>