ALTREE(1p)

✨ altree — the association + localisation tree queen ✨

okay bestie, sit DOWN, because altree is about to become your new hyperfixation 💅 this is the Perl program that runs Association and Localisation tests using phylogenetic Trees — yes, association with an A, localisation with an L, acronym slay 🌸

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🌈 SYNOPSIS

altree [options]

 Options:
    --version        program version
    --short-help|h   brief help message
    --help           help message with options descriptions
    --man            full documentation
    --association|a  perform the association test
    --s-localisation|l   perform the localisation using the S character
    --first-input-file|i result_file from phylogeny reconstruction programs
    --second-input-file|j file containing the nb of cases/controls carrying an haplotype
    --output-file|o output_file
    --data-type|t DNA|SNP
    --data-qual|q qualitative|quantitative
    --outgroup outgroup_name
    --remove-outgroup
    --tree-building-program|p phylip|paup|paml
    --splitmode|s nosplit|chi2split
    --no-prolongation
    --chi2-threshold|n value
    --permutations|r number
    --number-of-trees-to-analyse number
    --tree-to-analyse number
    --s-site-number number
    --s-site-characters ancestral state -> derived state
    --co-evo|e simple|double
    --print-tree
    --anc-seq ancestral sequence (only with phylip)
    --nb-files number of input files to analyse (only for association test)

like… look at all of those flags. it's giving buffet 🍓

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🎀 OPTIONS

• --version — prints the program version and then dips out (exits) 👋
• --short-help — prints a brief help message and exits, for when you're in a rush fr
• --help — prints a help message with the option descriptions, then exits. the full tea ☕
• --man — prints this whole manual page and exits. hi, that's us right now 🫶
• --association|a — performs the association test 🔥
• --s-localisation|l — localises the susceptibility locus using the "S-character method" 👑
• --first-input-file|i result_file — input file 1 (a paup, phylip or paml results file). if you're analysing several input files, their names have to be separated by colons. example: input1:input2 etc. no cap, colons only 💀
• --second-input-file|j correspond_file — input file 2, defaults to correspond.txt. the number of input file 2 has to match the number of input file 1, bestie — they're a matched set 🎀. the names of the different input file 2 also get separated by colons
• --output-file|o outfile — the output file ✨
• --data-type|t "DNA" | "SNP" — type of data: DNA (ATGCU) or SNP (0-1) 🧬
• --data-qual|q "qualitative" | "quantitative" — analyse qualitative (case/control) data or quantitative data
• --outgroup outgroup — root the tree with this outgroup 🌳
• --remove-outgroup — removes the outgroup of the tree before running the tests
• --tree-building-program|p "phylip" | "paup" | "paml" — which phylogeny reconstruction program was used
• --splitmode|s "nosplit" | "chi2split" — controls how tests are performed from one level to another
• --no-prolongation — no prolongation of branches in the tree 🚫🌿
• --chi2-threshold|n value — the significance threshold for chi2, default value 0.01
• --permutations|r number — number of permutations used to calculate exact p_values. (only for the association test, iykyk)
• --number-of-trees-to-analyse number — how many trees to analyse in the localisation analysis (only for the localisation method using S-character)
• --tree-to-analyse number — lets you specify exactly which tree to use instead of letting it pick randomly. can be used several times to specify multiple trees 🔁
• --s-site-number number — the number of the S character site in the sequence (only for the localisation method using S-character)
• --s-site-characters transition — character states for the S character, written as ancestral state -> derived state, e.g. G->C or 0->1 (only for the localisation method using S-character)
• --co-evo|e "simple" | "double" — type of co-evolution indice:
  • simple: only the anc -> der transition of S is used
  • double: the two possible transitions are used
• --print-tree — if you select this, the tree gets printed to the output 🌲✨
• --anc-seq anc_seq — lets you specify the ancestral sequence. this option is only useful when the tree is reconstructed using the mix program of phylip with the ancestral states specified in the file "ancestors"
• --nb-files number — lets you specify the number of input files (1 and 2) to analyse. this option only works for the association test.

⚠️ be careful bestie: if the number of trees isn't the same for the different input files, and the chosen tree doesn't exist in one file, the program won't work correctly 😭

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💖 DESCRIPTION

this program performs:

1. an association test between a candidate gene and disease, or a quantitative trait 💅
2. a localisation test: it detects which SNP is involved in the determinism of the disease or the quantitative trait 🔍

both of these tests are based on the analysis of haplotype phylogenetic trees. trees!! iconic behaviour, honestly 🦋

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okay that's the whole glow-up 🌈 this page was served to you courtesy of perl v5.42.3, dated 2026-08-20 — so yes, she's recent, she's maintained, she's thriving ✨ mwah, go run your trees bestie 💜