reconcile(1)

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

💖 reconcile(1) — bestie edition 💖

okay so you found the reconcile manual page (it lives in the General Commands Manual section, section 1, iykyk) and honestly? it's giving "small tool, big brain". let's get into it 🦋

✨ NAME ✨

reconcile — this program outputs the reconciliation that minimizes the number of duplications. that's the whole vibe. that's the assignment. 👑

🌸 SYNOPSIS 🌸

reconcile [OPTIONS] gene-tree species-tree [gene-species-map]

so you hand it a gene tree, a species tree, and optionally a gene-species-map, and it does its little magic. no cap. ✨

🎀 DESCRIPTION 🎀

okay bestie, listen: this program outputs the reconciliation that minimizes the number of duplications. literally that. that's the entire description. it's not being mysterious, it's just built different — it finds the reconciliation with the fewest duplications and prints it out. periodt. 💅

🫶 OPTIONS 🫶

  • --help — displays help (aka this very text). it's the "pls explain" button. 🙈
  • -V, --version — prints the version and then exits. quick little flex, then gone. ✨
  • -r, --reroot any|random|no — reroots the tree so the number of implied duplications/losses gets minimized — but only if the most parsimonious reconciliation is the one being chosen. the default is "no". so like, no rerooting unless you ask, bestie.
  • -w, --weights FLOAT FLOAT — sets the relative importance of duplications versus losses. first weight = duplications, second weight = losses. the default is 1.0,0.0, which counts duplications only. and heads up: the weights are required to be positive. no zeroes, no negatives, we don't do that here. 💀

⭐ EXIT STATUS ⭐

  • 0 — successful program execution. we ate. 🔥
  • 1 — some error occurred. it's giving "not today". 😭

🌈 URL 🌈

the prime-phylo home page: http://prime.sbc.su.se

🦋 SEE ALSO 🦋

primeDTLSR(1), primeDLRS(1), primeGEM(1), chainsaw(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1)

go read those too, they're all in the same friend group fr fr. 👑

and that's the whole page, bestie 💖 this one shipped as prime-phylo 1.0.11, dated 13 Mar, 2012 — vintage but iconic, main character energy forever, mwah 🎀✨

📦 where this page comes from