tree-mean-lengths(1)

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

🎀 NAME 🎀

okay so bestie, welcome to tree-mean-lengths — that's a section 1 manual page, aka a command you run in your terminal, and it's literally here to compute the mean lengths for branches in the given topology. that's the whole vibe. 💖

✨ SYNOPSIS ✨

tree-mean-lengths tree-file < in-file
yes queen, the tree goes in as an argument and the trees come in on stdin. that < is doing heavy lifting, don't skip it. 🫶

💅 DESCRIPTION 💅

compute the mean lengths for branches in the given topology.

that's it. that's the description. short, sweet, iconic. 🌸

🌈 ALLOWED OPTIONS: 🌈

  • -h, --help — produce help message. the classic. ask and ye shall receive. ✨
  • --tree arg — tree to re-root. 👑
  • -s arg (=0), --skip arg (=0) — number of tree samples to skip. default is 0, so no skipping unless you say so. 💅
  • -u arg, --until arg — Read until this number of trees. 🛑
  • --prune arg — Comma-separated taxa to remove. bye babes, you're out of the topology 🦋
  • -x arg (=1), --subsample arg (=1) — factor by which to subsample. defaults to 1, no subsampling energy. 🌸
  • --var — report standard deviation of branch lengths instead of mean. switching up the math, we love a plot twist 😭
  • --no-node-lengths — ignore branches not in the specified topology. 🙈
  • --safe — Don't die if no trees match the topology. emotionally supportive flag fr fr 🫶
  • --drop-partial — Remove partial branches. ✂️
  • --seed arg — random seed. 🎲
  • -V, --verbose — Output more log messages on stderr. the way that it just tells you everything 💀

🔥 REPORTING BUGS: 🔥

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

Please send bug reports to bali-phy-users@googlegroups.com.

found a bug? don't suffer in silence bestie, email the list. 💌

👑 AUTHORS 👑

Benjamin Redelings. that's the main character right there. ⭐

and that's the whole page!! this manual is from Feb 2018 and it's filed under tree-mean-lengths(1) — go forth and compute those means, you absolute icon. no cap, ily, bye 💜🧚

📦 where this page comes from