chainsaw(1)

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

💖 chainsaw(1) — cut a gene tree based on a reconciliation 💖

okay bestie, welcome to the General Commands Manual, section 1, where we talk about chainsaw 🪚✨. yes it's literally called chainsaw. no it does not cut wood. it cuts trees (the phylogenetic kind, bestie, keep up 💅).

🌸 NAME 🌸

chainsaw — cut a gene tree based on a reconciliation. that's it. that's the whole vibe. 🎀

✨ SYNOPSIS ✨

chainsaw [OPTIONS] reconciled-gene-tree  species-tree

two positional arguments, and they are not optional, so like… give her what she wants 🫶

🦋 DESCRIPTION 🦋

reconciled-gene-tree is the filename of the file containing trees in PRIME format. and here's the lil tea: the node id is optional ☕ — if you leave it out, all species nodes will be used recursively. so it's giving "do the whole thing, queen" 👑

species-tree is the species tree. yes that's really all it says. she's a tree. the species one. 🌳

💅 OPTIONS 💅

  • --help — Display help (this text). the classic. the icon. she shows you the manual you are currently reading 📖
  • -V, --version — Print version and exit. one and done, no notes 💫
  • -g, --guest-tree-format primeOrHybrid|inputxml — The input format. Default is primeOrHybrid. note that she said guest tree — that's the gene tree, bestie, don't @ me 🙈
  • -h, --host-tree-format primeOrHybrid|inputxml — The input format of the host tree. Default is primeOrHybrid. ⚠️ lowkey important: -h here is host-tree-format, NOT help. the help flag is --help with no short form. do not get got by this. i'm serious. 😭
  • -x, --node-name=STRING — A named species node to cut at. you give her a name, she cuts there ✂️
  • -i, --node-id=INT — The numerical id of a species node to cut at. same energy, but with numbers instead of names 🔢

🚦 EXIT STATUS 🚦

  1. 0 — Successful program execution. we ate and left no crumbs 🍽️✨
  2. 1 — Some error occurred. it's giving 💀 but it's fine, we move

🌈 URL 🌈

The prime-phylo home page: http://prime.sbc.su.se — go say hi, she's lovely 🫶

👀 SEE ALSO 👀

primeDTLSR(1), primeDLRS(1), primeGEM(1), showtree(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1) — the whole friend group, go follow them, iykyk 💜

bestie reminder: -h is host-tree-format. not help. i will not be repeating myself (i will be repeating myself). 🎀

and that's the page!! this one came from prime-phylo 1.0.11, dated 13 Mar, 2012 — vintage, iconic, still slaying. mwah 💋💖

📦 where this page comes from