QUICKTREE(1)

okay bestie, pull up a chair 🫶 you've landed on QUICKTREE(1), straight outta the User Commands section of the manual. no cap, this one's a lil chaotic but we're gonna get through it together, i promise 💅

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🌸 NAME 🌸

quicktree — transforms Stockholm alignment to PHYLIP phylogenetic tree

literally that's the whole job. it takes your alignment and it gives you a tree. iconic behavior honestly 🦋

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✨ SYNOPSIS ✨

quicktree [-options] <inputfile>

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💀 DESCRIPTION 💀

okay so. bestie. the entire description is this:

A Fatal Error occurred: No such option as '--help'.

not me getting personally attacked by the manpage itself 😭 like. that's it. that's the description. the vibe check was failed by whoever generated this page, and i have to respect it fr fr.

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👑 OPTIONS 👑

• -in <m|a> — tells quicktree what kind of input file it's getting: a distance matrix in phylip format (m), or an alignment in stockholm format* (a, which is the default, so if you say nothing it assumes a)
• -out <m|t> — tells it what to spit back out: a distance matrix in phylip format (m), or a tree in New Hampshire format (t)
• Advanced options — ✨ the spicy tier ✨
  • -upgma — Use the UPGMA method to construct the tree (it gets ignored for distance matrix outputs, so don't even try it there bestie)
  • -kimura — Use the kimura translation for pairwise distances (this one gets ignored for distance matrix inputs, so know your input type first 💅)
  • -boot <n> — Calcuate bootstrap values with n iterations (yes it says "Calcuate", i'm not fixing it, it's part of the lore 🎀) (ignored for distance matrix outputs)
  • -v — print version and exit

*Use sreformat, part of the HMMer package to convert your alignment to Stockholm format

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and then, because the universe loves a plot twist, here's the rest of that OPTIONS section, verbatim, in all its unhinged glory 🔥 — quicktree does not know what --version is and it is NOT being subtle about it:

A Fatal Error occurred: No such option as '--version'.  Usage: quicktree
[-options] <inputfile> Options: -in <m|a>        : input file is a
distance matrix in phylip format (m)

       or an alignment in stockholm format* (a, default)

-out <m|t>       : output is a distance matrix in phylip format (m) or

       a tree in New Hampshire format

Advanced options : -upgma           : Use the UPGMA method to construct
the tree

       (ignored for distance matrix outputs)

-kimura          : Use the kimura translation for pairwise distances

       (ignored for distance matrix inputs)

-boot <n>        : Calcuate bootstrap values with n iterations

       (ignored for distance matrix outputs)

-v               : print version and exit

*Use sreformat, part of the HMMer package to convert your alignment to
Stockholm format

so yeah. same options, second time, courtesy of a fatal error. the way that it just repeats itself?? main character energy but make it a crash message 🙈

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🔍 SEE ALSO 🔍

The full documentation for quicktree is maintained as a Texinfo manual. If the info and quicktree programs are properly installed at your site, the command

info quicktree

should give you access to the complete manual.

like, go read the real thing if you want the deep lore, bestie ⭐

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and that's the whole page, you ate it 💜 this manual page was brought to you by quicktree, dated October 2023, living its best life under the QUICKTREE(1) header. slay, go build a tree 🌈🧚💖