code: public static <C extends Sequence<D>, D extends Compound> Msa convert(
  			MultipleSequenceAlignment<C, D> msa) throws IOException {
  
  		// Convert the biojava MSA to a FASTA String
  		OutputStream os = new ByteArrayOutputStream();
  		FastaWriter<C, D> fastaW = new FastaWriter<C, D>(os,
  				msa.getAlignedSequences(),
  				new FastaHeaderFormatInterface<C, D>() {
  					@Override
  					public String getHeader(C sequence) {
  						return sequence.getAccession().toString();
  					};
  				});
  
  		fastaW.process();
  		String fastaMSA = os.toString();
  
  		// Parse the FASTA file in forester
  		return FastaParser.parseMsa(fastaMSA);
  	}
docs: Convert a BioJava {@link MultipleSequenceAlignment} to a forester
  {@link Msa}. The easiest way to convert them is writting the msa as a
  FASTA file and then parsing it with the forester {@link FastaParser}.
  
  @param msa
  BioJava MultipleSequenceAlignment
  @return forester Msa object
  @throws IOException
  if the conversion was not possible