PXSEQGEN(1)

📦
version 1.3.2 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

🌸 NAME 🌸

okay so bestie, welcome to pxseqgen — it's a sequence simulator under the GTR model. that's the whole vibe. it lives in section 1 of the User Commands manual, and it's lowkey iconic. 💅

✨ SYNOPSIS ✨

pxseqgen [OPTIONS]...

💖 DESCRIPTION 💖

so basically it's a basic sequence simulator under the GTR model. fr fr, that's what it does. it will happily take fasta, fastq, phylip, and nexus formats — either from a file or from STDIN. she's flexible like that. 🦋

👑 OPTIONS 👑

here's the whole menu, no gatekeeping:

  • -t, --treef=FILE — the input treefile, bestie. if you don't hand her one, she reads from STDIN instead. 🌳
  • -l, --length=INT — how long do you want your sequences to be? the default is 1000. 💫
  • -b, --basef=Input — comma-delimited base freqs, and the order is strictly A,C,G,T. default is equal. no favorites here. ⚖️
  • -g, --gamma=INT — gamma shape value. default is no rate variation, so if you want that spicy variation you gotta ask for it. 🌈
  • -i, --pinvar=FLOAT — proportion of invariable sites. default is 0.0. 📌
  • -r, --ratemat=Input — comma-delimited input values for the rate matrix. default is JC69, and the order is: A<->C,A<->G,A<->T,C<->G,C<->T,G<->T. don't shuffle it, i'm begging. 🔥
  • -w, --aaratemat=Input — comma-delimited amino acid rate matrix. default is all freqs equal, and the order is ARNDCQEGHILKMFPSTWYV. yes queen, memorize it. 🧬
  • -q, --aabasefreq=Input — AA frequencies, order: ARNDCQEGHILKMFPSTWYV. same lineup, different job. ✨
  • -c, --protein — run as amino acid. switching it up! 🍓
  • -n, --nreps=INT — number of replicates. how many times are we doing this, bestie? 🔁
  • -x, --seed=INT — random number seed. if you don't set one, she uses the clock otherwise. ⏰
  • -a, --ancestors — print the ancestral node sequences. default is no. and btw, use -p for the nodes labels. 👵
  • -p, --printnodelabels — print newick with internal node labels. default is no. 🌿
  • -m, --multimodel=Input — specify multiple models across the tree. the input goes like this:
A<->C,A<->G,A<->T,C<->G,C<->T,G<->T,Node#,A<->C,A<->G,A<->T,C<->G,C<->T,G<->T

and for example, EX:.3,.3,.3,.3,.3,1,.3,.3,.2,.5,.4 🎀

  • -k, --rootseq=STRING — set the root sequence. default is random (from basefreqs). 🌱
  • -o, --outf=FILE — output seq file, STOUT otherwise. (yes, that's literally what the page says 😭 STOUT. we don't question the ancestors.) 📤
  • -h, --help — display this help and exit. the classic. 🫶
  • -V, --version — display version and exit. 💜
  • -C, --citation — display phyx citation and exit. give credit where it's due, periodt. 📚

📚 CITATION 📚

if you're gonna use this, cite your sources bestie:

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

✍️ AUTHOR ✍️

Written by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim). legends, honestly. 👑

🐛 REPORTING BUGS 🐛

found a bug? don't suffer in silence, tell the devs:

Copyright © 2015-2024 FePhyFoFum License GPLv3

and that's the whole page bestie!! this was pxseqgen 1.3.1, from June 2024 — go simulate something gorgeous 💅✨🦋

📦 where this page comes from