ROGUENAROK-PARALLEL(1)

💖 ROGUENAROK-PARALLEL 💖

okay bestie, gather round, because this one is from the User Commands manual and it is lowkey a whole vibe. it's roguenarok-parallel, and it's here to find rogue taxa for you. no cap. let's get into it 🦋

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✨ NAME ✨

roguenarok-parallel — implements the RogueNaRok algorithm for rogue taxon identification (parallel version) 🎀

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🌸 DESCRIPTION 🌸

first thing's first, the page literally opens with this, and yes, we're keeping it exactly as it is, it's iconic in a cursed way:

roguenarok-parallel: invalid option -- '-'

okay moving on 💀

this is RogueNaRok version 1.0, released by Andre J. Aberer in 2011-10-25. an elder. a legend. a founding mother, if you will 👑

this program implements the RogueNaRok algorithm for rogue taxon identification. that's the whole assignment. that's the point.

here's the syntax, copy it, don't @ me:

SYNTAX: RogueNaRok -i <bootTrees> -n <runId> [-x <excludeFile>] [-c
<threshold>] [-b] [-s <dropsetSize>] [-w <workingDir>] [-h]

👑 OBLIGATORY 👑

these are the non-negotiables, bestie. you cannot skip these. it's giving mandatory.

• -i <bootTrees> — a collection of bootstrap trees. that's your input, your whole personality for this run 🌳
• -n <runId> — an identifier for this run. name your baby. give it an ID. it needs one 🏷️

🌈 OPTIONAL 🌈

these are the lil extras, the accessories to the outfit. optional but cute.

• -t <bestKnownTree> — if you've got a single best-known tree (like an ML or MP tree, iykyk) and you pass it in, RogueNaRok will optimize the bootstrap support in this best-known tree (still drawn from the bootstrap trees, don't worry). heads up though: the threshold parameter is ignored. periodt 🙈
• -x <excludeFile> — taxa listed in this file (one taxon per line, pls) will not be considered for pruning. they're safe. protected. untouchable 💅
• -c <threshold> — a threshold or mode for the consensus tree that gets optimized. give it a value between 50 (majority rule consensus) and 100 (strict consensus), or MR for the extended majority rule consensus. real talk: rogue taxa identified with respect to different thresholds can vary substantially, so choose with intention. DEFAULT: MR consensus ⭐
• -b — instead of trying to maximize the support in the consensus tree, RogueNaRok will try to maximize the number of bipartition in the final tree by pruning taxa. different goal, different girl. DEFAULT: off 🔥
• -L <factor> — a weight factor to penalize for dropset size. Factor=1 is Pattengale's criterion. the higher the value, the more conservative the algorithm is in pruning taxa. DEFAULT: 0.0 (=RBIC) ⚖️
• -s <dropsetSize> — maximum size of dropset per iteration. if dropsetSize == n, then RogueNaRok will test in each iteration which tuple of n taxa increases the optimality criterion the most, and prunes taxa accordingly. this improves the result, but runtimes will increase at least linearly. so like… better results, slower vibes. DEFAULT: 1 😭
• -w <workDir> — a working directory where output files are created. somewhere for the receipts to live 📁
• -T <num> — execute RogueNaRok in parallel with <num> threads. but bestie, listen: you need to compile the program for parallel execution first. no compiling, no threading 🧵
• -h — this help file. the classic. the MVP 🫶

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🎀 MINIMAL EXAMPLE 🎀

the bare minimum, the starter pack, the "just make it run":

MINIMAL EXAMPLE: ./RogueNaRok -i <bootstrapTreeFile> -n run1

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💜 AUTHOR 💜

this manpage was written by Nilesh Patra for the Debian distribution, and can be used for any other usage of the program. we love a flexible king 🫶

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and that's the whole page, bestie 💖 this was roguenarok-parallel 1.0.1, dated October 2021. go identify some rogue taxa, you absolute icon 🌟👑