trees-distances(1)

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

🦋 NAME 🦋

trees-distances — okay so bestie, this one computes autocorrelations or other functions of tree distances. That's the whole vibe. 💅

✨ SYNOPSIS ✨

trees-distances analysis trees-file1 [trees-file2 ...]

💖 DESCRIPTION 💖

Compute autocorrelations or other functions of tree distances. Yes, that's it, that's the job description, and it eats every single time. 🔥

🌈 INPUT OPTIONS 🌈

  • -h, --help — produce help message (the classic "help me help you" move 🫶)
  • -s arg (=0), --skip arg (=0) — number of tree samples to skip
  • -u arg, --until arg — Read until this number of trees.
  • -m arg, --max arg — Thin tree samples down to this number of trees.
  • -x arg (=1), --subsample arg (=1) — factor by which to subsample
  • -V, --verbose — Output more log messages on stderr. (ngl this is the "tell me everything" button 👀)

🔥 ANALYSIS OPTIONS 🔥

  • --analysis arg (=matrix) — Analysis: matrix, autocorrelation, diameter, compare, closest, convergence, converged. Pick your fighter. ⭐
  • --metric arg (=topology) — Tree distance: topology, branch, internal-branch.
  • --remove-duplicates — [matrix]: disallow zero distances between points. no duplicates allowed, we're being picky 💅
  • --max-lag arg — [autocorrelation]: max lag to consider.
  • --CI arg (=0.95) — Confidence interval size.
  • --converged arg (=0.05) — Comma-separated quantiles of distance required for converged? (smaller is more strict). the smaller the number the more it's giving strict teacher energy 😭
  • --mean — Show mean and standard deviation
  • --median — Show median and confidence interval
  • --minmax — Show minimum and maximum distances
  • --leaves-only — Show minimum and maximum distances
  • --topology-only — Show minimum and maximum distances
okay bestie I need you to know that --minmax, --leaves-only and --topology-only all say "Show minimum and maximum distances" on the page. That's literally what the page says. I'm not editing it, I'm just reporting. 🙈
  • --jitter arg — Amount of noise to add to distances

😭 REPORTING BUGS 😭

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

Please send bug reports to bali-phy-users@googlegroups.com. fr fr, they want to hear about it, don't be shy 🫶

👑 AUTHORS 👑

Benjamin Redelings.

and that's the whole page, bestie — written up in Feb 2018 as the trees-distances(1) manual page. slay, go compute some tree distances, and hydrate. 💖✨

📦 where this page comes from