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Algorithms for SP-optimal multiple alignments

Score functions

The sum-of-pairs (SP) function is defined as the sum of all pairwise scores between all pairs of letters in the columns of the multiple alignment:

$\begin{displaymath}\mathcal{S} (A) = \sum_{j=1}^N W(\vec{x}_j) \end{displaymath}$

with

$\begin{displaymath}W(\vec{x}_j) = \sum_{l < k} w(x_j^{(l)},x_j^{(k)}) \end{displaymath}$

Another possibility to define a score function is given by the Tree-Alignment-Score (see next section).

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