code: public double[][] getScoreMatrix() {
  		double[][] matrix = new double[sequences.size()][sequences.size()];
  		for (int i = 0, n = 0; i < matrix.length; i++) {
  			matrix[i][i] = scorers.get(i).getMaxScore();
  			for (int j = i+1; j < matrix.length; j++) {
  				matrix[i][j] = matrix[j][i] = scorers.get(n++).getScore();
  			}
  		}
  		return matrix;
  	}
docs: Returns the similarity matrix used to construct this guide tree.  The scores have not been normalized.
  
  @return the similarity matrix used to construct this guide tree