CreateOutDirForTrial allows creating the output directory for specific trial of the experiment using standard name.

WriteGenomeCytoscapeJSON is to write genome of the organism to the genomeFile in the outDir directory using Cytoscape JSON encoding.

WriteGenomeDOT is to write genome of the organism to the genomeFile in the outDir directory using DOT encoding.

WriteGenomePlain is to write genome of the organism to the genomeFile in the outDir directory using plain encoding.

WritePopulationPlain is to write genomes of the entire population using plain encoding in the outDir directory.