code: public static String toFASTA(MultipleAlignment alignment) {
  
  		// Get the alignment sequences
  		List<String> alnSequences = MultipleAlignmentTools
  				.getSequenceAlignment(alignment);
  
  		String fasta = "";
  		for (int st = 0; st < alignment.size(); st++) {
  			// Add the structure identifier as the head of the FASTA
  			fasta += ">" + alignment.getEnsemble().getStructureIdentifiers().get(st).getIdentifier()
  					+ "\n" + alnSequences.get(st) + "\n";
  		}
  		return fasta;
  	}
docs: Converts the {@link MultipleAlignment} into a multiple sequence alignment
  String in FASTA format.
  
  @param alignment
  MultipleAlignment
  @return String multiple sequence alignment in FASTA format
  @see MultipleAlignmentTools#getSequenceAlignment(MultipleAlignment)