PHIPACK-PHI(1)

👑 phipack-phi — the PHI test & friends 💅

okay bestie, listen up: this is the manual page for phipack-phi, a User Commands situation, and it's literally all about the PHI test and other tests of recombination. yes, recombination. we love a genome that can't stay in its lane. ✨

🌸 NAME 🌸

phipack-phi — the PHI test and other tests of recombination. no cap, that's the whole job description. 🧬

🎀 SYNOPSIS 🎀

Phi [-f|-s|-r] Filename  [-t] AlignmentType

like… that's the vibe. you hand it a Filename with one of -f, -s or -r, and optionally tell it the AlignmentType with -t. simple. iconic. periodt. 💖

🦋 DESCRIPTION 🦋

okay so first thing — if you did not specify an input file, this thing is gonna yell at you:

Input file not specified!!! (use -f|-r|-s)

not me forgetting the input file 💀 — yeah, don't be that girl. use -f, -r or -s.

and the other goodies you can tack on look like this:

[-p [#]] [-o] [-v] [-g [#]] [-b [#]]

heads up bestie: -b [#] shows up right there in the synopsis but there's no -b entry in the OPTIONS list below. so… it exists in spirit. do with that what you will. 🙈

✨ OPTIONS ✨

• -f — Filename is in FASTA format. classic. the blueprint. 💖
• -s — Filename is a Strict phylip file. strict as in no chill. 👑
• -r — Filename is a Relaxed phylip file. relaxed as in she's off the clock. 🌸
• -t — AlignmentType, and it's one of D|A|O where D=DNA, A=AA and O=OTHER. the default is DNA, so if you don't say anything it's gonna assume DNA. iykyk. 🧬
• -p — [#] runs the PHI permutation test. default is FALSE (as in, off), and #=1000. so it's giving "opt in, and here's your default number of permutations." ✨
• -w — # changes the default window size. default is w = 100. resize responsibly, bestie. 🪟
• -o — report other statistics — specifically NSS and Max Chi^2. default is FALSE, so she keeps those to herself unless you ask. 👀
• -v — Verbose mode. default is FALSE. turn it on and she will tell you everything. 💬
• -g — [i] prints the color (scaled) incompatibility matrix into graph.ppm. and i means Image only (no ticks...). default is FALSE. aesthetic output? we love to see it. 🖼️✨

reminder, fr fr: every default above is exactly as written — FALSE everywhere except -t (which defaults to DNA), -p's #=1000, and -w's 100. don't @ me. 💅

kisses, this was phipack-phi version 0.0.20160614 from August 2020 — and yeah, that's PHIPACK-PHI(1) in the footer, so you know it's official. 🫶💖 go forth and test some recombination, bestie, you got this. 🌈⭐