DLESSP(1)

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

💖 DLESSP(1) — User Commands 💖

okay bestie, sit down, grab a boba, because we're talking about dlessP and honestly? it's giving statistical main character energy. 🧚✨

✨ NAME ✨

dlessP — computes various p-values and other stats of interest for dless 💅

🌸 DESCRIPTION 🌸

so what does it do, you ask? it computes various p-values and other stats of interest for dless predictions, and then writes them all out to a tab-delimited file. slay. 🎀

and here's the part where you have to feed it the right stuff, no cap:

  • the alignment and tree.mod arguments should be exactly as given to DLESS 🫶
  • and predictions.gff should be the output of DLESS — like, it's literally DLESS's whole thing, don't try to hand it something else 😭

🔥 OPTIONS 🔥

💜 alignment vibes

  • --msa-format, -i FASTA|PHYLIP|MPM|MAF|SS — the alignment format. default is to guess the format from the file contents (iconic, honestly). and psst — the program msa_view can be used for conversion if you need to switch things up 🦋

💜 reference sequence era

  • --refseq, -M <fname> — (for use with --msa-format MAF) reads the complete text of the reference sequence from <fname> (that's FASTA format, bestie) and combines it with the contents of the MAF file to produce a complete, ordered representation of the alignment. also important: the reference sequence of the MAF file is assumed to be the one that appears first in each block. periodt. 💅
  • --refidx, -r <refseq_idx> — use the coordinate frame of the specified sequence in the output. default value is 1, which is the first sequence in the alignment; 0 indicates the coordinate frame of the entire multiple alignment. pick your fighter 🎀

💜 output & extras

  • --timing, -t <file> — write timing data to <file>. lowkey useful, highkey underrated ⏱️
  • --html, -H <dirname> — creates a directory and writes one HTML file into it per DLESS prediction, giving the stats for that prediction. so like, one file per prediction, all cute and organized in its own little dir. we love a structured queen 👑
  • --help, -h — shows this help message and exits. the classic escape hatch, no notes 🙈

🫶 a lil sign-off 🫶

this whole page? it's dlessP version 1.4, dated May 2016 — and that's the source/version tea, delivered with love. 💖 now go compute those p-values, bestie, you got this. ✨🌸💅

📦 where this page comes from