PHIPACK-PROFILE(1)

📦 version 0.0.20160614, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

👑 PHIPACK-PROFILE 👑

okay bestie, welcome to phipack-profile, section 1 of the User Commands manual 💅 this is the tool that runs the PHI test plus a whole lil squad of other recombination tests, and she is iconic for it ✨

🌸 NAME 🌸

phipack-profile — PHI test and other tests of recombination 🧬🦋

✨ SYNOPSIS ✨

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

💖 DESCRIPTION 💖

okay so here's the thing, if you don't hand her a file she will literally yell at you:

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

and then she hits you with the rest of the vibe check:

[-w #] [-k #] [- v] [-n #] [-m #]

no cap, she needs to know which file and what kind of alignment it is before anything fun can happen 🙈

🎀 OPTIONS 🎀

  • -f — Filename = FASTA format 🍓
  • -s — Filename = Strict phylip file 💜
  • -r — Filename = Relaxed phylip file 🌈
  • -t — AlignmentType = D|A|O where D=DNA, A=AA and O=OTHER [default DNA] 🧬
  • -w — # = Change default window size for PHI [default w = 100] 🪟
  • -v — Verbose [default = FALSE] 👀
  • -n — # = Change scanning size for regions to test [default n = 1000] 🔍
  • -m — # = Step size for profile method [default m = 25] 👟

that's the whole thing, bestie, go run your recombination tests and slay 💅✨

signing off: this was phipack-profile version 0.0.20160614, dated August 2020 🎀 mwah, ily, bye 🫶

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