code: private void saveHistory(String folder) throws IOException {
  
  		String name = msa.getStructureIdentifier(0).getIdentifier();
  		FileWriter writer = new FileWriter(folder + name
  				+ "-symm_opt.csv");
  		writer.append("Step,Time,RepeatLength,RMSD,TMscore,MCscore\n");
  
  		for (int i = 0; i < lengthHistory.size(); i++) {
  			writer.append(i * saveStep + ",");
  			writer.append(timeHistory.get(i) + ",");
  			writer.append(lengthHistory.get(i) + ",");
  			writer.append(rmsdHistory.get(i) + ",");
  			writer.append(tmScoreHistory.get(i) + ",");
  			writer.append(mcScoreHistory.get(i) + "\n");
  		}
  
  		writer.flush();
  		writer.close();
  	}
docs: Save the evolution of the optimization process as a csv file.