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Algorithms for SP-optimal multiple alignments



The problem

Given the sequences s(1), s(2),...,s(n). Find an optimal alignment Aopt which maximizes $ \mathcal{S} (A) \ $:

\begin{displaymath}\mathcal{S}(A^{opt}) = \mathcal{S}^{opt}(s^{(1)}, s^{(2)},...,s^{(n)}) \end{displaymath}

$ \mathcal{S}(A^{opt}) $ is the optimal alignment-score. Note that there may be several optimal alignments for a set of sequences, while, of course, the optimal alignment score is unique.




Comments are very welcome.
luz@molgen.mpg.de