PXMONO(1)

💖 pxmono — the monophyly checker 💖

okay bestie, listen. this is pxmono, and it's literally the vibe check for your tree 🧚✨

---

✨ SYNOPSIS ✨

pxmono [OPTIONS]...

---

🌸 DESCRIPTION 🌸

so basically? monophyly checker. that's the whole thing, that's the gig 💅

it takes a newick- or nexus-formatted tree, either from a file or straight from STDIN, and it goes to work. no cap 🫶

---

🎀 OPTIONS 🎀

• -t, --treef=FILE — the input tree file. if you don't give one, it's reading from STDIN instead 🌈
• -n, --names=CSL — the names, separated by commas. and i need you to hear me when i say: NO SPACES! not one. not even a lil one. periodt 💀
• -f, --namesf=FILE — you'd rather put the names in a file? iconic. one name per line, bestie 📄✨
• -c, --comp — takes the complement, aka it checks the monophyly of the taxa that are not in your list. the opposite girlies 🔄
• -i, --ignore — ignore missing names. because the default? the default is to exit if the names aren't in the tree. harsh but fair 😭
• -o, --outf=FILE — output tree file. if you skip it, it goes to STOUT instead 🍓
• -h, --help — display this help and dip out 👋
• -V, --version — display the version and dip out 🦋
• -C, --citation — display the phyx citation and dip out 📚

---

💜 CITATION 💜

if you use this, 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. main character energy, honestly ✨

---

🐛 REPORTING BUGS 🐛

found a bug? not the cute kind?? report it to: <https://github.com/FePhyFoFum/phyx/issues>

phyx home page: <https://github.com/FePhyFoFum/phyx>

we will handle it, no stress 🫶

---

🌈 COPYRIGHT 🌈

Copyright © 2019-2024 FePhyFoFum License GPLv3

---

and that's the whole page bestie!! this was pxmono 1.3.1, born into the world in June 2024 🎀 go check some monophyly, you got this 💖🌸🦋