PXBOOT(1)

💖 PXBOOT 💖

okay bestie, so this is pxboot — it lives in section 1 of the manual (that's the "User Commands" girlypop zone, iykyk) and it does sequence alignment bootstrap or jackknife resampling. literally the main character of resampling tools 💅

---

✨ NAME ✨

pxboot — sequence alignment bootstrap or jackknife resampling 🦋

---

🌸 SYNOPSIS 🌸

pxboot [OPTIONS]...

---

🎀 DESCRIPTION 🎀

okay so here's the vibe: this is sequence alignment bootstrap or jackknife resampling. periodt. 💖

it will happily eat fasta, fastq, phylip, and nexus formats — from a file or from STDIN, whichever you're feeling 🌈

and the results? written in fasta format. slay. ✨

---

👑 OPTIONS 👑

• -s, --seqf=FILE — input sequence file. if you don't hand it one it'll just read from STDIN instead, no biggie 🫶
• -p, --partf=FILE — file listing empirical partitions, and the format is NAME = START-STOP[\INTERVAL] 💅
• -f, --frac=DOUBLE — jackknife percentage. the default is bootstrap, which is literally just -f 1.0 🎀
• -x, --seed=INT — random number seed. if you skip it, it uses the clock instead ⏰
• -o, --outf=FILE — output sequence file. otherwise it goes to STOUT 🙈 (that's what the manpage says, bestie, don't come for me)
• -h, --help — display this help and exit 👋
• -V, --version — display version and exit ⭐
• -C, --citation — display phyx citation and exit 📜

---

📚 CITATION 📚

if you're gonna cite it (and you should, it's giving academic royalty 👑), here's the whole thing verbatim:

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 💜

---

🐛 REPORTING BUGS 🐛

found a bug? no cap, please tell someone:

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

---

💀 COPYRIGHT 💀

Copyright © 2013-2024 FePhyFoFum

License GPLv3

---

ngl bestie, that's the whole page. go forth and resample responsibly 🌸

and yeah — this is pxboot 1.3.1, dated June 2024. that's the tea ☕💖