code: public boolean isSkipped() {
          // --no-phaseIII is the same as:
          // --no-gene-scaffolding --no-named-complexes --no-protein-families --no-orthology
          return (hasOption(NO_P3_LONG_OPT) || (hasOption(NO_GS_LONG_OPT)
                  && hasOption(NO_NC_LONG_OPT) && hasOption(NO_PF_LONG_OPT)
                  && hasOption(PHASE3_NO_ORTHOLOGY_LONG_OPTION)));
      }
docs: Determine whether phase III will be skipped (such as with the --no-phaseIII
  command line option).
  
  @return