necom Documentation

Add comments to node(s) in a Newick file.

Input:

• A Newick tree file.

Notes:

• Comments are stored in an NHX-like format (:key=value).
• For named nodes, use --node.
• For unnamed internal nodes, use --lca with two comma-separated names, e.g. --lca A,B.
• Use --string / -s to add a free-form string stored under the string property.
• Visualization options:
  • --color, --label, and --comment-text (--comment) each take one argument.
  • --dot, --bar, --rec, and --tri take zero or one argument. When no value is supplied they use their default color (see below); any other value is passed through as the color directly.
• Defaults when no color is given:
  • --dot / --bar: black
  • --rec: LemonChiffon
  • --tri: white
• Predefined colors for --color, --dot, and --bar:
  • red (188,36,46)
  • black (26,25,25)
  • grey (129,130,132)
  • brown (121,37,0)
  • green (32,128,108)
  • purple (160,90,150)
  • blue (0,103,149)
• Predefined background rectangle colors for --rec:
  • LemonChiffon (251,248,204)
  • ChampagnePink (253,228,207)
  • TeaRose (255,207,210)
  • PinkLavender (241,192,232)
  • Mauve (207,186,240)
  • JordyBlue (163,196,243)
  • NonPhotoBlue (144,219,244)
  • ElectricBlue (142,236,245)
  • Aquamarine (152,245,225)
  • Celadon (185,251,192)
• --remove / -r scans all nodes and removes whole property entries whose serialized key=value (or bare key) matches the regex.

Examples:

1. Add a string comment to a node necom nwk comment tree.nwk --node A --string "bootstrap 90" -o out.nwk

2. Add a colored dot to an internal node via LCA necom nwk comment tree.nwk --lca A,B --dot red -o out.nwk