How to get the score of two alignments?

[aadimator]

Is there a way to only get the score of two alignments? Let's say that I have two alignments; "MQD--RV--KRP" and "MKKL-K-K-H-P" and I want to get there score. Currently, I'm trying to do:

scoremodel = AffineGapScoreModel(BLOSUM62, gap_open=-3, gap_extend=-1)
res = pairalign(GlobalAlignment(), S1, S2, scoremodel, score_only=true)

But this is giving me an error because of - present in the S1 and S2 sequences. Is there a way to only compute the score of different alignments, without actually aligning them? I have a list of alignments already computed and I want to compute their scores only. Any help/guidance would be much appreciated.