MAF-SORT(1)

📦
version 1654 · 7 versions
, in ubuntu stonking

💅 MAF-SORT(1) 💅

okay bestie, welcome to maf-sort, a lil User Commands girlie whose whole entire job is sorting MAF-format alignments by sequence name. that's it. that's the gig. she's simple, she's effective, she's iconic 🎀

✨ NAME ✨

maf-sort — sort MAF-format alignments by sequence name 🦋

like... she literally takes your alignments and puts them in sequence-name order. main character behavior only.

🌸 SYNOPSIS 🌸

maf-sort [options] my-alignments.maf

you hand her a MAF file, she hands you back vibes (sorted vibes). you can also throw some options at her first if you want to be extra 💅

👑 OPTIONS 👑

  • -h — shows this help message and then exits. the classic "wait what does this do again" button, no shame in pressing it, we've all done it 🙈
  • -d — only print duplicate alignments. like, just the dupes. only the duplicates. nothing but the duplicates. if you're on a quest for copy-paste energy, this is your flag fr fr 💀
  • -n — sort by the n-th sequence. the default is 1, so if you don't say anything she's sorting by the first sequence, no questions asked. give her a different number and she'll sort by that one instead ✨
no cap: -n takes a number for the n-th sequence, and the default is 1. don't overthink it, bestie 🫶

🧚 the cute lil sign-off 🧚

and that's the whole page!! this is maf-sort version 1654, dated August 2026, and honestly she ate 💖 go sort something, you got this, slay, periodt 🌈⭐

📦 where this page comes from