let command_list () =
  [
    "visualization", [
      "fat", (fun () -> new Guppy_fat.cmd ());
      "heat", (fun () -> new Guppy_heat.cmd ());
      "sing", (fun () -> new Guppy_sing.cmd ());
      "tog", (fun () -> new Guppy_tog.cmd ());
    ];

    "statistical comparison", [
      "bary", (fun () -> new Guppy_bary.cmd ());
      "squash", (fun () -> new Guppy_squash.cmd ());
      "kr_heat", (fun () -> new Guppy_kr_heat.cmd ());
      "kr", (fun () -> new Guppy_kr.cmd ());
      "epca", (fun () -> new Guppy_epca.cmd ());
      "lpca", (fun () -> new Guppy_lpca.cmd ());
      "pmlpca", (fun () -> new Guppy_pmlpca.cmd ());
      "splitify", (fun () -> new Guppy_splitify.cmd ());
      "edpl", (fun () -> new Guppy_edpl.cmd ());
      "rarefact", (fun () -> new Guppy_rarefact.cmd ());
      "error", (fun () -> new Guppy_error.cmd ());
      "fpd", (fun () -> new Guppy_fpd.cmd ());
      "unifrac", (fun () -> new Guppy_unifrac.cmd ());
      "indep_c", (fun () -> new Guppy_indep_c.cmd ());
      "mcl", (fun () -> new Guppy_mcl.cmd ());
    ];

    "classification", [
      "classify", (fun () -> new Guppy_classify.cmd ());
      "to_rdp", (fun () -> new Guppy_to_rdp.cmd ());
    ];

    "utilities", [
      "round", (fun () -> new Guppy_round.cmd ());
      "demulti", (fun () -> new Guppy_demulti.cmd ());
      "to_json", (fun () -> new Guppy_to_json.cmd ());
      "distmat", (fun () -> new Guppy_distmat.cmd ());
      "merge", (fun () -> new Guppy_merge.cmd ());
      "filter", (fun () -> new Guppy_filter.cmd ());
      "info", (fun () -> new Guppy_info.cmd ());
      "redup", (fun () -> new Guppy_redup.cmd ());
      "adcl", (fun () -> new Guppy_adcl.cmd ());
      "mft", (fun () -> new Guppy_mft.cmd ());
      "islands", (fun () -> new Guppy_islands.cmd ());
      "compress", (fun () -> new Guppy_compress.cmd ());
      "trim", (fun () -> new Guppy_trim.cmd ());
      "ograph", (fun () -> new Guppy_ograph.cmd ());
      "check", (fun () -> new Guppy_check.cmd ());
      "rarefy", (fun () -> new Guppy_rarefy.cmd ());
      "to_csv", (fun () -> new Guppy_to_csv.cmd ());
      "placemat", (fun () -> new Guppy_placemat.cmd ());
    ];
  ]
