WARG(1)

💖 WARG — bestie edition 💖

okay so this is the manual for warg, a.k.a. WARG(1), living in the User Commands section of your friendly neighborhood man pages. it infers homologous recombination in bacteria using whole genome sequences, and honestly? she's iconic for it. let's get into it 🧬✨

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✨ NAME ✨

warg — inference of homologous recombination in bacteria using whole genome sequences. yes, that's the whole vibe. no cap. 🦋

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🌸 SYNOPSIS 🌸

warg [OPTIONS] treefile datafile outputfile

three files, bestie. you feed her a tree, some data, and she hands you an output. slay. 💅

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👑 DESCRIPTION 👑

so here's the lore: bacteria, unlike us, can reproduce on their own. main character behavior tbh. but they also have mechanisms that transfer DNA between organisms — that whole process is formally called recombination. 💫

the mechanisms by which recombination takes place have been studied extensively in the laboratory, but lowkey so much remains to be understood: how, when, and where recombination happens inside natural populations of bacteria, and how it helps them adapt to new environments. that's the mystery arc. 🔍

ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. it's giving time-travel detective but for DNA. 🕵️♀️🧬

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💅 OPTIONS 💅

• -w NUM — sets the number of pre burn-in iterations. default is 100000. warm-up era 💫
• -x NUM — sets the number of burn-in iterations. default is 100000. still warming up, girl 🎀
• -y NUM — sets the number of iterations after burn-in. default is 100000. now we're actually cooking 🔥
• -z NUM — sets the number of iterations between samples. default is 100. 👀
• -T NUM — sets the value of theta. use sNUM instead of NUM for per-site. tiny s, big difference ✨
• -R NUM — sets the value of rho. use sNUM instead of NUM for per-site. same rule, bestie 🌈
• -D NUM — sets the value of delta. that's it, that's the option 🫶
• -s NUM — use the given seed to initiate the random number generator. determinism girlies rise 🎲
• -S NUM,SEED — run on a subset of NUM regions determined by seed SEED.
  • NUM/NUM/../NUM — run on a specified region(s) given by each NUM. slice it up 🍰
• -r NUM — perform r tempered steps between topological updates. default: 0. ❄️🔥
• -t NUM — tempered at "temperature" t for topological updates. default: 1.0. it's giving thermostat but make it phylogenetics 🌡️
• -U — start from a UPGMA tree, rather than the default random tree. structured queen 👑
• -G NUM — greedily compute the "best fit" tree, given the recombination observed on the current tree. if NUM is negative and a previous run is provided, the tree is calculated from all observed values. if NUM is positive, a "greedy move" is performed with weight NUM (see -a).

⚠️ note that this is NOT an MCMC move and causes bias. bestie, she said what she said 💀

• -a NUM,...,NUM — set the ELEVEN (real valued) move weightings to the given vector, with weightings separated by commas (NOT SPACES). the weightings need not sum to 1, but must be in the following order:
  1. MoveRho (ignored if not needed)
  2. MoveDelta (ignored if not needed)
  3. MoveTheta (ignored if not needed)
  4. MoveRemEdge
  5. MoveAddEdge
  6. MoveSiteChange
  7. MoveTimeChange
  8. MoveEdgeChange
  9. MoveAgeClonal
  10. MoveScaleTree
  11. MoveRegraftClonal

eleven. count them. eleven. no spaces. i'm serious 🙈

• -i NUM,...,NUM — set the SIX parameters for creating random Recombination Trees under the inference model. the parameters are:
  • N (integer) — the number of sequences in the sample. default 10.
  • n_B (integer) — the number of block boundaries in the sample. default 8.
  • l_B (integer) — the length of each block: L=n_B * l_B. default 500.
  • delta (real) — the average length of imports. default 500.0.
  • theta (real) — the mutation rate NOT per site. default 100.0.
  • rho (real) — the recombination rate NOT per site. default 50.0.

six parameters, six little legends 🧚

• -f — forbid topology changes, (allowing updates of coalescence times). hands off the tree shape 🚫🌳
• -v — verbose mode. she will talk. a lot. 💬
• -h — this help message. hi bestie 🫶
• -V — print Version info. the receipts 📜

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🎀 AUTHOR 🎀

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. king behavior, honestly 👑

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and that's the whole page, babe! this was warg version 1.0, dated December 2017. she's been serving since 2017 and she's still that girl 💖✨ slay, hydrate, and always read the manpage before you run the command. periodt. 🌸🦋💅