tree-tool(1)

📦
version 4.1 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 tree-tool — the manual, but make it cute 💖

okay bestie, so this is tree-tool(1), a lil command-line baddie that does stuff to Newick trees. Sit down, grab a boba, we're doing phylogenetics today 🧚✨

✨ NAME ✨

tree-tool — Perform various operations on Newick trees.

Like. That's the whole vibe. It does operations. On trees. Newick ones. 🌳

🌸 SYNOPSIS 🌸

tree-tool tree-file [OPTIONS]

You give it a tree-file, you give it some OPTIONS, and it goes to work. That's it. That's the whole thing. 🫶

👑 DESCRIPTION 👑

Perform various operations on Newick trees.

fr fr, that's the mission statement. Now here's the good stuff — the options are split into three lil cliques: general, modification, and output. Pick your fighters. 💅

✨ GENERAL OPTIONS ✨

  • -h, --help — produce help message. The classic. When in doubt, ask for help. Self-care honestly.
  • -V, --verbose — Output more log messages on stderr. She's chatty and she's proud of it. Not me running this every single time for the drama 😭

💅 MODIFICATION OPTIONS 💅

These ones change your tree. Main character energy. Handle with care, bestie.

  • --prune arg — Comma-separated taxa to remove. Say goodbye to those little guys 👋
  • --root — Find a root position. Where does the tree even start?? We're figuring it out.
  • --resolve — Resolve polytomies. Untangling the mess, we love to see it.
  • --remove-root-branch — Remove single branch from root.
  • --remove-root-branches — Ensure root is not a tip.
  • --remove-knuckles — Remove degree-2 nodes. Knuckle removal!! Sounds violent, is actually just tidying 🎀
  • --scale arg — Scale branch-lengths by factor. Stretch her out or shrink her down, your call.
  • --strip-internal-names — Remove internal node names. No names, only vibes.
  • --name-all-nodes — Add node names. Opposite energy. Everybody gets a name now, slay 👑

🌈 OUTPUT OPTIONS 🌈

These ones just tell you things. No tree was harmed. Observation only, periodt.

  • --length — Report the total tree length.
  • --diameter — Report the tree diameter.
  • --count-leaves — Show the number of leaves.
  • --count-nodes — Show the number of nodes.
  • --show-leaves — Show the leaf names.
  • --show-nodes — Show the node names.

🐛 REPORTING BUGS 🐛

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com. Don't be shy, they're nice, and also they can't fix what they don't know about 💜

🫶 AUTHORS 🫶

Benjamin Redelings. The icon. The legend. The moment. 👑

ngl if something's broken, tell the group chat (that email up there) instead of just suffering in silence. iykyk 💀

this page was brought to you by the Feb 2018 release of tree-tool(1) — yes she's a little vintage, and yes she still ate 💖✨🎀

📦 where this page comes from