if you want to use scoring matrices you need to use a different specialization of our Score class. To use scoring schemes like the Pam or Blosum matrices you need to use the following code:
Score<int, ScoreMatrix<AminoAcid, Pam120_> > scorePam120(gap, gapOpen);
You can also use our shortcuts to make the code look nicer. You can find a list of all available shortcuts here: http://docs.seqan.de/seqan/1.4.1/SPEC_Score+_Matrix.html.
For the example above this would look like:
Pam120 scorePam120(gap, gapOpen);
I hope that will solve your problem!
On Feb 17, 2014, at 12:32 AM, Samuel Flores <firstname.lastname@example.org> wrote: