PHYLONIUM(1)

📦
version 1.7 · 2 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

👑 PHYLONIUM — the manual page, bestie edition

okay so you opened the phylonium(1) manual and honestly? iconic decision. this is the phylonium manual, and i'm gonna walk you through every single line of it like we're texting at 2am. no skips. no "you'll figure it out." we're doing this together 💖

✨ NAME ✨

phylonium — rapidly estimate evolutionary distances

like, rapidly. fast. slay.

🌸 SYNOPSIS 🌸

phylonium [OPTIONS...] FILES...

that's it. that's the whole vibe. options, then files. periodt.

🦋 DESCRIPTION 🦋

so phylonium estimates the evolutionary distance between closely related genomes. closely related, bestie — don't go throwing wildly unrelated stuff at it and expecting magic.

here's how it works: phylonium reads the input sequences from FASTA files and computes the pairwise evolutionary distance. and this part is important so i'm saying it loud — all sequences in one file are considered to be contigs of the same genome. one file = one genome. don't forget it, i'm begging 🫶

💅 OUTPUT 💅

the output is a symmetrical distance matrix in PHYLIP format, and every entry is a divergence value written as a positive, real number.

  • a distance of zero means the two sequences are identical
  • every other value is an estimate for the nucleotide substitution rate (Jukes-Cantor corrected)

now for the part nobody likes 😭 — for technical reasons the comparison might fail and no estimate can be computed at all. when that happens, nan gets printed. and what does that mean?

nan means the input sequences were either too short (<200bp) or too diverse (K>0.5) for our method to work properly. it's not you, it's the math. 💀

🎀 OPTIONS 🎀

buckle up, we're going through all of them, no skipping 🧚

  • -2, --2pass — after a first run, a 'central' sequence is chosen as reference for the second pass. this improves accuracy when the first reference is an outgroup. two passes, double the glow ✨
  • -b INT, --bootstrap=INT — compute multiple distance matrices, with n-1 bootstrapped from the first. see the paper Klötzl & Haubold (2016) for a detailed explanation. stats girlies rise 🫶
  • -r FILE — define the reference sequence.
  • -t INT, --threads=INT — the number of threads to be used; by default, all available processors are used. multithreading is only available if phylonium was compiled with OpenMP support. so if it's not going fast... that might be why 🙈
  • -p FILE — print the reference positions to the given path. also sets complete deletion.
  • --progress[=WHEN] — print a progress bar. WHEN can be 'auto' (default if omitted), 'always', or 'never'. progress bar = serotonin, honestly.
  • -v, --verbose — prints additional information, including the amount of found homology. apply multiple times for extra verboseness. stack it, bestie, more -v = more lore 🔥
  • -h, --help — prints the synopsis and an explanation of available options.
  • --version — outputs version information and acknowledgments.

Copyright © 2017 - 2023 Fabian Klötzl

License GPLv3+: GNU GPL version 3 or later.

this is free software: you are free to change and redistribute it. there is NO WARRANTY, to the extent permitted by law. the full license text is available at <http://gnu.org/licenses/gpl.html>.

no warranty bestie, i don't make the rules 💜

🌈 ACKNOWLEDGMENTS 🌈

giving credit where credit is due, as we always should 👑

  1. Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f.
  2. SA construction: Mori, Y. (2005). Short description of improved two-stage suffix sorting algorithm.
  3. Bootstrapping: Klötzl, F. and Haubold, B. (2016). Support Values for Genome Phylogenies
  4. Phylonium: Klötzl, F. and Haubold, B. (2020). Phylonium: Fast Estimation of Evolutionary Distances from Large Samples of Similar Genomes

😭 BUGS 😭

Reporting Bugs

please report bugs to <fabian-phylonium@kloetzl.info>.

like actually report them, don't just suffer in silence, that's not the vibe 🫶

and that's the whole page, bestie. this was phylonium version 1.7, dated 2023-03-16, from the phylonium manual. go forth and estimate some evolutionary distances, you absolute main character 💖✨🦋

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