alignments-diff(1)

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

✨ alignments-diff(1) ✨

Okay bestie, meet alignments-diff 🦋 It's the tool that lines up two alignments so you can compare them side by side. Literally iconic.

💖 SYNOPSIS 💖

alignments-diff alignment-file1 alignment-file2 [OPTIONS]

🌸 DESCRIPTION 🌸

Okay so the whole point is: alignments-diff takes two alignments and aligns them for comparison. No cap, that's the entire job 💅

🎀 GENERAL OPTIONS 🎀

  • -h, –help — Pops out a help message for you 🫶

🧚 INPUT OPTIONS 🧚

  • –alphabet arg — Set it to Codons' if you want codon alphabets to be preferred. Main character energy 👑

🦋 OUTPUT OPTIONS 🦋

  • –merge — Stacks both alignments into one big alignment, and the names end up duplicated. Lowkey chaotic but it works ✨
  • –dual — Writes out the two aligned alignments separately, one at a time 🍓
  • –fill arg (=gap) — Fills the blank columns with either gap or unknown. The default is gap 🫧
  • -d arg, –differences-file arg — Filename where the differences get saved, in AU format 💜
  • –blocksize arg (=20) — How wide the blocks of same-colored stuff are. The default is 20 🌈
  • –classes arg (=1) — Number of groups for the non-matching characters. The default is 1 ⭐

🐛 REPORTING BUGS 🐛

Bugs happen, it's giving human. Check out the BAli-Phy online help at http://www.bali-phy.org/docs.php 💀

Then send your bug reports to bali-phy-users@googlegroups.com. The devs want to hear from you 🫶

👑 AUTHORS 👑

Written by Benjamin Redelings. Absolute legend 🔥

Okay that's the tea ☕ This page is alignments-diff(1), dated Feb 2018. Stay iconic and go compare some alignments 💅🌸✨

📦 where this page comes from