ALTREE-ADD-S(1p)

✨ NAME ✨

altree-add-S — so the actual name field literally just says Title... bestie, no cap, that's what's in there 💀 we're not gonna pretend otherwise.

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🦋 SYNOPSIS 🦋

altree-add-S [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 data concerning the trait (qualitative or quantitative)
    --output-file|o       output file
    --epsilon|e           epsilon value
    --data-type|t         data type: SNP or DNA
    --proportion|p        proportion of cases in the sample (for qualitative data only)
    --data-qual|q         data type: qualitative or quantitative
    [--outgroup|g]        name of the outgroup
    --low|l               if an haplotype is present equal or less than -l times, the state of S will be set to "?"

That's the whole menu, verbatim, no crumbs left over 🍓

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💖 OPTIONS 💖

okay so here's every single flag, one by one, no skipping, we don't do that here 🫶

• --version — prints the program version and then dips out. ✨
• --short-help — a brief help message, and then it's gone. 💅
• --help — a help message with the options descriptions spelled out, then exits.
• --man — prints the whole manual page and then exits. iconic behavior honestly 👑
• --first-input-file|i — Input file 1, and it's a paup or phylip file 🧚
• --second-input-file|j — Input file 2, which holds either the number of times a given haplotype is carried by case and control individuals (that's the qualitative data situation) or the quantitative values correqsponding to a givent haplotype (the quantitative data situation). yes bestie, we keep that spelling exactly as it landed, character for character 🙈
• --output-file|o — the Output file, where the good stuff goes 🌸
• --epsilon|e — the espilon parameter (peep the formula over in the documentation) 💜
• --data-type|t — what kind of data are we dealing with: DNA (ATGCU) or SNP (0-1)
• --proportion|p — the proportion of case individuals in the sample
• --outgroup|g — the name of the outgroup, but only if it's not already sitting in the file that has the number of cases and controls per haplotype 👀
• --data-qual|q — tells the program whether the data are qualitative or quantitative
• --low|l — if a haplotype shows up equal to or less than -l times, then the state of S gets set to "?" 💀

heads up: --outgroup|g is the optional one, which is why it's wrapped in brackets up in the synopsis. everything else is just... there. periodt.

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🌈 DESCRIPTION 🌈

This program adds a brand new character — we call it "character S" — onto every single haplotype in the input file. How does it decide? Based on the number of cases and controls carrying that haplotype. that's the whole plot bestie, and it ate 💅

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and that's the tea, fr fr 💖 this lil page came to you courtesy of the User Contributed Perl Documentation corner of the world, version perl v5.42.3, dated 2026-08-20, filed under ALTREE-ADD-S(1p). go forth and annotate those haplotypes, bestie 🦋 slay ✨