alignment-draw(1)

📦
version 4.1 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ alignment-draw(1) ✨

Okay bestie, this is alignment-draw(1) 🦋 and it's giving HTML alignment realness 💅

🎀 NAME 🎀

alignment-draw is how you draw an alignment to HTML, and you can optionally color the residues by AU 🌈

🧚 SYNOPSIS 🧚

alignment-draw alignment [AU file] [OPTIONS]

💖 DESCRIPTION 💖

Okay so the whole point is drawing an alignment to HTML 🌸 and if you want, it can color residues by AU. Iconic, honestly.

🔥 GENERAL OPTIONS 🔥

  • -h, --help — pulls up the help message, obviously 🙈
  • --file arg — the file with your sequences and initial alignment 🍓
  • --legend — prints a legend showing how the color-scheme shows uncertainty ✨
  • --show-ruler — prints a ruler so you can see column numbers 📏
  • --column-colors — color-codes the column ticks by column certainty 🌈
  • --AU arg — the file with alignment uncertainties 🦋
  • --show-gaps arg (=yes) — shows the gaps (default is yes) 💜
  • --show-letters arg (=yes) — shows the letters (default is yes) 🫶
  • --show-names arg (=yes) — shows the names (default is yes) 👑
  • --gaps-different arg (=yes) — colors the gaps grey, so they don't blend in 🩶 (default is yes)
  • --width arg — how many columns go on each line 🎀
  • --start arg — the first column to plot 🌸
  • --end arg — the last column to plot 🌸
  • --format arg (=HTML) — the format you want the plot in, and it defaults to HTML 💅
  • --min arg — the minimum value of the scale function 🧚
  • --max arg — the maximum value of the scale function 🧚
  • --color-scheme arg — throws in a length showing how certainties map to colors 🌈
  • --scale arg (=LOD) — the scale for the uncertainties, defaulting to LOD ⭐

🌈 EXAMPLES 🌈

Bestie, check out this vibe:

Rainbow+contrast+fade AA+contrast+fade+fade+fade+fade

🙈 REPORTING BUGS 🙈

Lowkey the best place to get help is the BAli-Phy online help at http://www.bali-phy.org/docs.php. 🌸

If something's broken, send your bug reports to bali-phy-users@googlegroups.com 💌

👑 AUTHORS 👑

This was all made by Benjamin Redelings. Slay 💖

Anyway, that's the whole page, bestie 🫶 It's the alignment-draw(1) manual from Feb 2018, so go make some pretty alignments 🦋✨

📦 where this page comes from