MAKEHKY(1)

📦 version 1.8, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

makeHKY — ok so bestie, this one Generates an HKY tree model, given kappa (the transition/transversion … and then the sentence literally just ends there 💀 no cap, that's the whole NAME line, it trails off mid-thought. We move.

🌸 DESCRIPTION 🌸

So what this lil icon does: it Generates an HKY tree model, given kappa (that's the transition/transversion rate ratio). Periodt.

And like, you get to pick two more things on top of that:

  • the equilibrium base composition, and
  • either a branch length or a whole complete tree

…and you specify those with the options down below. That's the vibe. 🦋

✨ OPTIONS ✨

  • --gc, -g <val> — Sets the base composition from a G+C composition you give it, assuming P(A)=P(T) and P(C)=P(G). The default? 0.4. Cute, lowkey balanced, we love.
  • --pi, -p <pi_A,pi_C,pi_G,pi_T> — Overrides --gc and lets you define the base composition explicitly, queen. Heads up tho: your values will be renormalized so they sum exactly to one. So don't stress about your math, it'll fix it for you 💅
  • --branch-length, -t <val> — Assumes a tree that's just a single branch of the length you specify. Default is 1. One branch, one dream. 🌱
  • --tree, -T <tree.nh> — Overrides --branch-length and uses the tree you hand it instead. Full tree energy, main character behavior 👑
  • --help, -h — Displays this help message and dips. That's it, that's the whole job 🫶
🎀 Real talk: --pi beats --gc, and --tree beats --branch-length. If you set both of a pair, the override one is the one that shows up to the party. iykyk.

And that's the whole page bestie, we ate and left zero crumbs ✨ This little love letter is makeHKY version 1.4, dated May 2016, and it lives in the User Commands section of your manual. Go build a tree, you gorgeous genius 🌈⭐🧚💜

📦 where this page comes from