ALTREE-CONVERT(1p)

📦
version 1.3.2 · 7 versions
, in ubuntu stonking

💅 ALTREE-CONVERT 💅

okay so bestie, welcome to altree-convert, part of the User Contributed Perl Documentation crew 🫶. This is a <pink>Perl</pink> script and this is its manual page, section 1p. Strap in, it's giving "niche genetics tool but make it cute" energy 🧬✨

🌸 NAME 🌸

altree-convert - Title...

yeah bestie the description literally says "Title..." 😭 that's what the original says so that's what we're keeping, no cap. iconic honestly.

🎀 SYNOPSIS 🎀

altree-convert [options]

Options:
   --version             program version
   --short-help|h        brief help message
   --help                help message with options descriptions
   --man                 full documentation
   --first-input-file|i  input file 1
   --second-input-file|j input file 2 (not mandatory)
   --output-file|o       output file
   --case-control-output|c  output containing the nb cases/controls
   --data-type|t         DNA|NUM
   --phylo-prog|p        PAUP|PHYLIP
   --reconstruct-prog|r  PHASE|FAMHAP
   --data-quali|q        Type of data: qualitative or quantitative
   --nbind-threshold|s   Minimum number of individuals ecquired to keep an haplotype

✨ OPTIONS ✨

  • --version — prints the program version and then dips out. bye 👋
  • --short-help — prints a lil brief help message and exits. snack-sized help 🍓
  • --help — prints a help message with the options descriptions, then exits. the full meal deal fr fr.
  • --man — prints the manual page and exits. (hi, that's this 💖)
  • --first-input-file|i — Input file 1 (this one's the output of the haplotype reconstruction program 👑)
  • --second-input-file|j — Input file 2 (the second output of famhap, or a file containing the disease status). optional bestie, not mandatory!
  • --output-file|o — Output file. the whole point tbh 💅
  • --case-control-output|c — Output file that holds the number of cases and controls carrying each haplotype. not me keeping track of everyone's business 📊
  • --data-type|t "DNA"|"SNP" — Type of data: DNA (ATGCU) or SNP (0-1). pick your fighter 🌈
  • --phylo-prog|p "phylip"|"paup" — Phylogeny reconstruction program. which one's your main character?
  • reconstruct-prog|r "famhap|phase" — Haplotype reconstruction program. yes the missing dashes are literally in the original, I don't make the rules 🙈
  • data-quali|q "qualitative|quantitative" — Type of data analyzed. (also living dash-free, as the original intended ✨)
  • nbind-threshold|s — Minimal number of individuals carrying an haplotype recquired to keep it for further analysis. If you want to keep all haplotypes, you must affect 0 to this variable.
heads up bestie: that last one is the "do I keep this haplotype or not" gatekeeper 🚪 if you set it too high you're gonna lose haplotypes, and the only way to keep literally all of them is smacking a 0 in there. no cap.

🦋 DESCRIPTION 🦋

This program will read the given input file(s) and generate an input file for the phylogenetic reconstruction software paup or phylip/paml. that's it, that's the job, and it ate 🔥

and that's the whole page bestie, you're so welcome 💖

this was perl v5.42.3, dated 2026-08-20 — mwah, take care, go convert some haplotypes, ily 🎀✨👑

📦 where this page comes from