KALIGNFMT(1)

✨ NAME ✨

kalignfmt — Global and progressive multiple sequence alignment 🧬💅

okay so real talk, this is the alignment bestie. It takes your sequences and lines them up so you can actually see what's going on. No cap.

kalignfmt-avx2 -i <seq file> -o <out aln>

Kalign (3.3.4) 👑

That's the whole description, bestie. The version is doing all the talking here. Not me being lazy, it's just what the page says, periodt.

--format — The output format you want. Default is [Fasta]. It's giving classic, honestly.
--reformat — Takes an existing alignment and reformats it. Default is [NA].
--changename — Renames your sequences to 1 .. N. Clean, numbered, iconic. Default is [NA].
--unalign — Strips out all the gaps and writes it out to fasta. Default is [NA].
--clean — Does extra checks on the alignment. Being thorough? We love to see it. Default is [NA].
--version (-V/-v) — Prints the version. Default is [NA].

Passing sequences via stdin: (yes, piping, we stan a flexible input 🫶)

cat input.fa | kalign -f fasta > out.afa

Combining multiple input files: (multiple files at once, main character energy fr fr)

kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa

This program comes with ABSOLUTELY NO WARRANTY 😭 — for details type:

`kalign -showw'

This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. 💜

Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795

like pls cite it, it's the least you can do for the alignment of your dreams ✨

that's the whole vibe check, bestie — kalignfmt 3.3.4, November 2022. go align something iconic 💖🦋✨

📦 where this page comes from