MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> multipleSequenceAlignment= new MultipleSequenceAlignment <ProteinSequence, AminoAcidCompound>();
       List<AlignedSequence<ProteinSequence,AminoAcidCompound>> alSeq=profile.getAlignedSequences();
       Sequence` seq;` `       ProteinSequence pSeq;` `       for (int i=0; i<alSeq.size(); i++){` `     ` `           seq=alSeq.get(i);` `           pSeq=new ProteinSequence(seq.getSequenceAsString(),seq.getCompoundSet());` `           pSeq.setAccession(seq.getAccession());` `           multipleSequenceAlignment.addAlignedSequence(pSeq);` `              ` `       }`