PXUPGMA(1)

💖 pxupgma — UPGMA tree generator 💖

okay bestie, welcome to pxupgma, section 1 of the User Commands manual, and she is exactly what she says on the tin: a bare bones UPGMA tree generator. no frills, no drama, just vibes and trees. 🌳✨

---

✨ SYNOPSIS ✨

pxupgma [OPTIONS]...

that's it. that's the whole invocation. she takes options and she goes. 💅

---

🌸 DESCRIPTION 🌸

so like. bare bones UPGMA tree generator. that's literally the whole pitch, no notes. 🫶

right now — and this is important, bestie — she only uses uncorrected p-distances. that's the whole distance situation. no corrections, no glow-ups, just raw p-distances. periodt.

she'll happily take fasta, fastq, phylip, and nexus formats, and she'll take them from a file or from STDIN. so whether you're piping or pointing at a file, she's eating. 😌🍓

---

🎀 OPTIONS 🎀

• -s, --seqf=FILE — your input sequence file goes here, bestie. and if you don't hand her one? she reads from STDIN instead. no file, no problem. 💜
• -o, --outf=FILE — this is where the newick file gets written. and if you don't give her an output file, she writes to STOUT instead. (yes, STOUT. that's what the page says. i don't make the rules, i just report them faithfully. 😭)
• -h, --help — shows you this help and then dips. exit stage left. 👋
• -V, --version — shows you the version and then dips. same energy. ✨
• -C, --citation — shows you the phyx citation and then dips. academic queen behaviour. 👑

---

👑 CITATION 👑

if you use this in your work, cite the girlies, fr fr:

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

---

🦋 AUTHOR 🦋

Written by Joseph W. Brown, Joseph F. Walker. icons, honestly. 💅

---

💀 REPORTING BUGS 💀

found a bug? not me finding a bug 🙈 — go tell them here:

• Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
• phyx home page: <https://github.com/FePhyFoFum/phyx>

---

🌈 COPYRIGHT 🌈

Copyright © 2015-2021 FePhyFoFum License GPLv3

---

and that's the whole page, bestie! 🎀 this was pxupgma 1.2, dated June 2021, straight outta the User Commands manual. go build some trees. slay. 🌳💖✨