ROGUENAROK-SINGLE(1)

✨ NAME ✨

roguenarok-single — bestie, this is the single core version of the tool that implements the RogueNaRok algorithm for rogue taxon identification 🦋

🌸 DESCRIPTION 🌸

okay so first thing, if you run it with nothing, it's gonna yell at you:

ERROR: Please specify a file containing bootstrap trees via -i.

💀 not me getting read to filth by a phylogenetics program. anyway.

This is RogueNaRok version 1.0, released by Andre J. Aberer in 2011-10-25 👑

This program implements the RogueNaRok algorithm for rogue taxon identification. that's the whole vibe, no cap ✨

🎀 SYNTAX 🎀

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

💅 OBLIGATORY 💅

these ones you literally cannot skip, bestie:

• -i <bootTrees> — a whole collection of bootstrap trees. your main character input 🌳
• -n <runId> — an identifier for this run. just a lil name tag so you know which run is which 🏷️

🫶 OPTIONAL 🫶

the fun extra stuff, lowkey iconic:

• -t <bestKnownTree> — if you've got a single best-known tree (like an ML or MP tree) you can hand it over and RogueNaRok will optimize the bootstrap support in that best-known tree instead (and yes, it's still drawn from the bootstrap trees, don't worry). heads up: the threshold parameter gets ignored when you do this. periodt.
• -x <excludeFile> — taxa listed in this file (one taxon per line) will not be considered for pruning. like a do-not-touch list 🙈
• -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). ngl, rogue taxa identified with respect to different thresholds can vary substantially, so choose wisely. 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. 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 gets about 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. it does improve the result, but runtimes will increase at least linearly, so like… be aware 😭 DEFAULT: 1
• -w <workDir> — a working directory where output files are created 📁
• -T <num> — execute RogueNaRok in parallel with <num> threads. note that you need to compile the program for parallel execution first, so it's giving "read the room" energy 🧚
• -h — this help file. your bestie when you're lost 💖

🌈 MINIMAL EXAMPLE 🌈

the absolute bare minimum to get her going:

./RogueNaRok -i <bootstrapTreeFile> -n run1

💜 AUTHOR 💜

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. slay 🎀

and that's the whole thing bestie!! roguenarok-single 1.0.1, dated October 2021 — go identify some rogue taxa, you got this 👑✨🦋