if you only need the score without traceback then MeyersBitVector would be the choice. You can use the MeyersHirschberg version to get the traceback too. Note that both versions can only be applied to an edit distance cost scheme.
For more complex scoring schemes you need the NeedlemanWunsch algorithm. Have a look at our tutorial pages to find out all about the alignment algorithms in SeqAn: http://trac.seqan.de/wiki/Tutorial/PairwiseSequenceAlignment.
The NeedlemanWunsch also works with the globalAlignmentScore function. In fact it computes no traceback at all, speeding up the algorithm a lot.
On Aug 21, 2013, at 1:55 PM, Johannes Dröge <firstname.lastname@example.org>