code: public SubstitutionMatrix<AminoAcidCompound> getSubstitutionMatrix() {
  		if ( substitutionMatrix == null){
  			substitutionMatrix = SubstitutionMatrixHelper.getMatrixFromAAINDEX(DEFAULT_SUBSTITUTION_MATRIX);
  
  		}
  		return substitutionMatrix;
  	}
docs: Sets the  substitution matrix to be used for influencing the alignment with sequence conservation information.
  Default: SDM matrix (Prlic et al 2000)
  @return substitutionMatrix