- ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
- sm = configureScoreModel(sm);
- tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+ ScoreModelI sm = configureScoreModel(pwtype);
+ tree = new NJTree(av, type, sm, SimilarityParams.Jalview);