reroot(1)

📦 version 1.0.11, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 reroot(1) 💖

okay bestie, so this one lives in the General Commands Manual section, and it's called reroot — and yeah, it does exactly what it says on the tin. 🎀

✨ NAME ✨

reroot — compute a (new) root for the tree. like, it goes and finds your tree a whole new root. glow-up for your phylogeny fr fr 🌳👑

🦋 SYNOPSIS 🦋

reroot [OPTIONS] tree-file

🌸 DESCRIPTION 🌸

So here's the vibe: this program reroots the trees in <treefile> on a selected edge. That's it. That's the whole personality. 💅

The default is to output a random rerooting — chaos, but make it scientific 🎲✨ — but you can also choose to give it the edge to put the root on, or an outgroup, or even all possible rootings (iconic, unhinged, love that for us).

Output gets written to stdout unless the exhaustive rooting is chosen. In that case -o is giving the prefix for filenames to use, and the results are written to <prefix>_<n>.tree, where <n> is the node number of the head of the edge. 🗂️

Warning! In the current implementation, all time/length info is lost. 😭 like it's gone. bye. not coming back. so don't come crying to me when your branch lengths ghost you 👻

🎀 OPTIONS 🎀

  • --help — Display help. your lil "what do I do now" button 🫶
  • -V, --version — Print version and exit. short and sweet, no notes 👑
  • -S, --read-tree-from-stdin — read tree from STDIN (no <tree-file>). pipe it in bestie, no file needed 🍓
  • -f, --input-format prime|inputxml — The input format. Default is prime. pick your flavor 🌈
  • -e, --exhaustive — Do all possible rootings. go absolutely feral, do every single one 💀
  • -o, --output-file-prefix file-prefix — The stem for filenames. this is the lil name-prefix everything gets built on ✨
  • -n, --node-index INT — Reroot tree at edge leading to node. you point, it roots 🎯
  • -g, --outgroup STRING — Root tree at smallest subtree containing the leaves listed in a commaseparated arguments. yes, comma-separated, no spaces required, just vibe it out 🌱

💜 EXIT STATUS 💜

  • 0 — Successful program execution. we ate. 🎉
  • 1 — Some error occurred. it's giving oops 😭

🌟 URL 🌟

The prime-phylo home page: http://prime.sbc.su.se — go be nosy, it's fine 💻✨

🧚 SEE ALSO 🧚

primeDTLSR(1), primeDLRS(1), primeGEM(1), chainsaw(1), reconcile(1), showtree(1), tree2leafnames(1), treesize(1) — the whole friend group, go say hi 🫶

and that's the page babes!! this one came from prime-phylo 1.0.11, dated 13 Mar, 2012 — vintage, lowkey, still slaying 💖🌸 periodt.

📦 where this page comes from