RUN_GUBBINS(1)

📦 version 3.4.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

okay bestie, pull up a chair 🫶 this is the manual page for run_gubbins, a User Commands situation, and it is so much cooler than it sounds. it builds phylogenies. for bacteria. while dealing with recombination. no cap. 💖

✨ NAME ✨

run_gubbins — phylogenetic analysis of genome sequences 🌈 that's it, that's the whole name section, she's concise and she knows it 💅

🦋 SYNOPSIS 🦋

run_gubbins [-h] [--outgroup OUTGROUP] [--starting_tree STARTING_TREE]
[--use_time_stamp] [--verbose] [--no_cleanup] [--tree_builder
TREE_BUILDER] [--iterations ITERATIONS] [--min_snps MIN_SNPS]
[--filter_percentage FILTER_PERCENTAGE] [--prefix PREFIX] [--threads
THREADS] [--converge_method CONVERGE_METHOD] [--version]
[--min_window_size MIN_WINDOW_SIZE] [--max_window_size MAX_WINDOW_SIZE]
alignment_filename

yes she has a LOT of flags. she's a maximalist. we respect it. ✨

🌸 DESCRIPTION 🌸

okay so. Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. literally the whole point. 🦠✨

and in case you were wondering what the name even means (I know you were, bestie, I know you): Gubbins stands for Genealogies Unbiased By recomBinations In Nucleotide Sequences 👑 it's an algorithm that iteratively identifies loci containing elevated densities of base substitutions, while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. the way that she does both at the same time?? multitasking queen fr fr 💅

and the simulations?? they demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution — and she can run in only a few hours on alignments of hundreds of bacterial genome sequences. not slow. not messy. iconic behaviour only. 🔥

💅 OPTIONS 💅

🎀 positional arguments:

  • alignment_filename — the Multifasta alignment file. that's your input bestie, hand it over 🫴

⭐ optional arguments:

  • -h, --help — shows this help message and dips out. classic. exit stage left 💀
  • --outgroup OUTGROUP, -o OUTGROUP — the Outgroup name for rerooting. and here's the cute part: a list of comma separated names can be used if they form a clade 🧚 so like, one name, or a whole little clade squad, your call.
  • --starting_tree STARTING_TREE, -s STARTING_TREE — Starting tree. give her a head start 🌱
  • --use_time_stamp, -u — Use a time stamp in file names. so you can tell your runs apart, unlike your exes ⏰
  • --verbose, -v — Turn on debugging. she gets chatty. we love a talkative queen 🗣️
  • --no_cleanup, -n — Don't cleanup intermediate files. hoarder mode activated, the intermediate files stay 🗂️
  • --tree_builder TREE_BUILDER, -t TREE_BUILDER — Application to use for tree building [raxml|fasttree|hybrid], default RAxML. pick your fighter 🥊
  • --iterations ITERATIONS, -i ITERATIONS — Maximum No. of iterations, default is 5. she loops, she refines, she slays 🔁
  • --min_snps MIN_SNPS, -m MIN_SNPS — Min SNPs to identify a recombination block, default is 3 🧬
  • --filter_percentage FILTER_PERCENTAGE, -f FILTER_PERCENTAGE — Filter out taxa with more than this percentage of gaps, default is 25. bye to the gappy ones, no offence 🚪
  • --prefix PREFIX, -p PREFIX — Add a prefix to the final output filenames. branding, babes 🎀
  • --threads THREADS, -c THREADS — Number of threads to run with RAxML, but only if a PTHREADS version is available. read that twice bestie 👀
fr fr, that --threads caveat is real: it only does anything if you've got a PTHREADS build. no PTHREADS, no threading, don't come for me.
  • --converge_method CONVERGE_METHOD, -z CONVERGE_METHOD — Criteria to use to know when to halt iterations [weighted_robinson_foulds|robinson_foulds|recombination]. how does she know when to stop? one of these three tells her 🛑
  • --version — show program's version number and exit. the classic flex 💁‍♀️
  • --min_window_size MIN_WINDOW_SIZE, -a MIN_WINDOW_SIZE — Minimum window size, default 100 🪟
  • --max_window_size MAX_WINDOW_SIZE, -b MAX_WINDOW_SIZE — Maximum window size, default 10000 🪟✨

📚 SEE ALSO 📚

the receipts, bestie — she is peer reviewed and everything 🧾:

Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196.

like, doi: 10.1093/nar/gku1196, she's in the literature, she's cited, she's that girl 📖💅

🫶 AUTHOR 🫶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, we appreciate you 🥹🌸

and that's the whole vibe check, bestie 💖 this was run_gubbins version 2.0.0, dated Julu 2016 (yes, Julu, I'm just the messenger 🫣), filed under RUN_GUBBINS(1). go build a tree, you've got this. periodt. 👑✨

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