TREE_RECON(1)

📦
version 2.5.2 · 2 versions
, in ubuntu stonking

🧬 TREE_RECON(1) — the tree_recon girlies are BACK

okay so bestie, welcome to tree_recon 💖 it's a manual page, it's a whole vibe, and by the end of this you're gonna be building phylogenetic trees like it's nothing. no cap. the manual name is TREE_RECON(1) and iykyk 🫶

✨ NAME ✨

tree_recon — Tree reconstruction 🌳 like literally reconstructing trees. main character energy fr fr.

🌈 SYNOPSIS 🌈

tree_recon [OPTIONS] -m IN.DIST

that's it. that's the whole summoning ritual 💅 <italic>OPTIONS</italic> go in the front, and -m IN.DIST is the non-negotiable at the end.

🦋 DESCRIPTION 🦋

so what does this lil icon do? it Reconstructs a phylogenetic tree from a Phylip matrix IN.DIST. that's the whole thing. it takes your distance matrix and gives you a tree back 🎀 obsessed honestly.

💅 OPTIONS 💅

  • -h, --help — shows you the help message when you're lost. no shame, we've all been there 🙈
  • --version — tells you the version info. iconic for flexing ⭐

🍓 Input / Output:

  • -m, --matrix INPUT_FILE — the name of your Phylip distance matrix file. gotta have at least three species in there, bestie, three's the minimum (no two-species trees, that's not a tree that's a situationship). the valid filetype is: .dist ✨
  • -o, --out-file OUTPUT_FILE — where you want the output to land. valid filetypes are: .newick and .dot 💖 Default: tree.dot.

🧚 Algorithm Options:

  • -b, --build STRING — which tree-building method you wanna use, and omg the options:
    • nj: neighbour-joining 👑
    • min: UPGMA single linkage
    • max: UPGMA complete linkage
    • avg: UPGMA average linkage
    • wavg: UPGMA weighted average linkage

and here's the tea ☕ Neighbour-joining creates an unrooted tree. but like, we root that tree at the least joined pair. periodt.

valid values are one of nj, min, max, avg, and wavg. Default: nj 🌸

💌 CONTACT AND REFERENCES 💌

got questions? got comments? wanna slide into an inbox?

For questions or comments, contact:

  • Tobias Rausch <rausch@embl.de> 💜

SeqAn Homepage:

kbd tip bestie: smash Ctrl+C when you need out. and fr fr, read the valid filetypes before you yell at the terminal, it's not the terminal's fault 🫶

and that's the page!! this was tree_recon 1.4.12 [tarball] being an absolute legend 💀✨ mwah, go build some trees 💖🌳

📦 where this page comes from