BASE_EVOLVE(1)

📦 version 1.8, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 BASE_EVOLVE 💖

okay bestie, so this is base_evolve — a lil User Commands icon from the BASE_EVOLVE(1) manual, and she is here to serve you a synthetic alignment like it's nothing. 🧬✨

🌸 NAME 🌸

base_evolve — Produce a synthetic alignment by simulating evolution according to

✨ DESCRIPTION ✨

Produce a synthetic alignment by simulating evolution according to a phylogenetic model or a phylo-HMM. That's the whole vibe. 🦋

She deals with base-substitution only, not indels — so if you were hoping for insertions and deletions, not today, bestie. 🙈

And here's the tea: if you give her multiple tree models, then you must also hand her an HMM file showing how to transition between them. No HMM, no transition, no alignment. Periodt. 💅

🎀 EXAMPLE 🎀

like, literally just do this:

       base_evolve --nsites 500 mytree.mod > simulated.fa

       base_evolve --nsites 500 simple-gene.hmm tree1.mod tree2.mod \
       tree3.mod --features simulated2.gff --catmap simple-gene.cm \ >
       simulated2.fa

look at her go 🔥

👑 OPTIONS 👑

  • --nsites, -n <nsites> — Generate an alignment with <nsites> columns. Default is 1000. (a thousand columns is the default, she's generous like that 💖)
  • --msa-format, -o FASTA|PHYLIP|MPM|SS — Output alignment in specified format. Default is FASTA. pick your format, pick your fighter ✨
  • --features, -f <out.gff> — (for use with a phylo-HMM) Output an annotations file in GFF reflecting the path through the phylo-HMM. she's literally documenting her own journey through the HMM, main character energy fr fr 🌈
  • --catmap, -c <map.cm> — (for use with --features) Use specified category map to define feature names. so like, the names gotta come from somewhere 🎀
  • --embed, -e <alt.mod>,<length> — Embed an artificial element of the given length in the alignment, drawing columns from <alt.mod>. A single element is embedded in the exact middle of the generated alignment. Useful for testing sensitivity of methods for functional element detection. 🧚 she's putting a lil mystery element right in the center, dead center, for science
  • --help, -h — Display this help message and exit. the classic. the icon. 🫶
ngl, no cap: those tree models without an HMM file? that's a no. give her the HMM. 😭

and that's the whole page, bestie 💜 this was base_evolve version 1.4, from May 2016, and yes she's still that girl. mwah. 💅🌸✨

📦 where this page comes from