String[] seqs = new String[] { "FKL", "R D", "QIA", "GWC" };
ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
- MatrixI pairwise = sm.findSimilarities(seqs);
+ MatrixI pairwise = sm.findSimilarities(seqs, SimilarityParams.Jalview);
/*
* should be NxN where N = number of sequences