code: public static <C extends Sequence<D>, D extends Compound> DistanceMatrix fractionalDissimilarity(
  			MultipleSequenceAlignment<C, D> msa) throws IOException {
  
  		Msa fMsa = ForesterWrapper.convert(msa);
  		DistanceMatrix DM = PairwiseDistanceCalculator
  				.calcFractionalDissimilarities(fMsa);
  
  		return DM;
  	}
docs: The fractional dissimilarity (D) is defined as the percentage of sites
  that differ between two aligned sequences. The percentage of identity
  (PID) is the fraction of identical sites between two aligned sequences.
  
  <pre>
  D = 1 - PID
  </pre>
  
  The gapped positons in the alignment are ignored in the calculation. This
  method is a wrapper to the forester implementation of the calculation:
  {@link PairwiseDistanceCalculator#calcFractionalDissimilarities(Msa)}
  
  @param msa
  MultipleSequenceAlignment
  @return DistanceMatrix
  @throws Exception