PHYUTILITY(1)

📦 version 2.7.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 PHYUTILITY(1) 💖

okay bestie, welcome to the phyutility manual page — it lives in section 1 of the User Commands manuals, and it's literally your girl for tree and sequence glow-ups. pull up a chair 🫶

✨ NAME ✨

phyutility — tools for manipulating sequences and phylogenies 🌳🧬

🌸 SYNOPSIS 🌸

phyutility <command> <options>

🦋 DESCRIPTION 🦋

Phyutility is a command line program that performs simple analyses or modifications on both trees and data matrices. no cap. it's giving "one binary, all the vibes" 💅

👑 OPTIONS 👑

To get help on a specific command use option -h <command> — yes queen, every command has its own little help menu, just ask her directly.

🎀 COMMANDS 🎀

for trees 🌳

  • consensus — Calculate consensus trees. Use like -con -t <threshold> -in <infile> -out <outfile>. this is the "everyone agree on one tree please" button ✨
  • convert — Convert tree files. Use like -vert -in <infile> -out <outfile>. (and yes, the short flag is -vert, that's not a typo, that's just her little quirk 😭)
  • leafstab — Leaf stability index calculation. Use like -ls -in <infile>. telling you which leaves are the main characters fr fr
  • linmove — Lineage movement calculation. Use like -lm -names <tip names> -tree <consensus> -in <infile> -out <outfile>. tracking which lineages are wandering off 🚶♀️
  • prune — Prune lineages. Use like -pr -names <tip names> -in <infile> -out <outfile>. ✂️ bye bestie
  • reroot — Reroot trees. Use like -rr -names <tip names> -in <infile> -out <outfile>. changing who's the main character of the tree 💅
  • thin — Thin trees. Use like -tt # -in <infile> -out <outfile>. decluttering, but make it phylogenetics 🧹
  • treesupp — Support for a set of trees. Use like -ts -tree <tree> -in <infile> -out <outfile>. how much do the girlies back you up 👑

for seqs 🧬

  • clean — Trim seqs based on threshold. Use like -clean # -in <infile> -out <outfile> -aa <to force aa>. glow-up your alignment ✨
  • concat — Concatenate alignments. Use like -concat -in <infiles> -out <outfile> -aa <to force aa>. putting all your lil files in one big file, slay 🫶
  • ncbiget — Fetch seqs from NCBI. For options run phyutility -h ncbiget. go get your sequences bestie 🏃♀️
  • ncbisearch — Search NCBI. For options run phyutility -h ncbisearch. 🔍
  • parse — Parse genbank results. For options run phyutility -h parse. turning that raw output into something usable 💖

🌈 EXAMPLE 🌈

phyutility -con -t 0.5 -in testall.tre -out test.con

Consensus the set of trees in testall.tre collapsing branches with less than 0.5 frequency.

phyutility -vert -in test.tre -out testvert.nex

Convert the tree file from newick in test.tre into nexus in testvert.nex.

phyutility -concat -in test.aln test2.aln -out testall.nex

Concatenate 2 alignment files into nexus in testall.nex.

⭐ SEE ALSO ⭐

See documentation at https://github.com/blackrim/phyutility/blob/master/manual.pdf?raw=true for more information. (iykyk, the manual pdf is right there if you need the deep lore 📖)

💜 AUTHOR 💜

Stephen A. Smith http://www.blackrim.org eebsmith@umich.edu — the icon who made all this happen 👑

and that's the whole page bestie, you ate 💅✨

this lil number ships as Debian, version 2.7.3 — so like, if you're on Debian, that's the flavor you're getting 🎀 mwah, go consensus something 💖

📦 where this page comes from