KALIGN(1)

📦
version 3.5.1 · 2 versions
  • 3.5.1 · debian bookworm, debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking (latest)
  • 3.3.1 · ubuntu jammy
, in debian bookworm, debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 KALIGN(1) 💖

okay bestie, welcome to the kalign page — it lives in the User Commands section of the manual, and it's about to be your new fave 🫶

✨ NAME ✨

kalign — Global and progressive multiple sequence alignment. that's it, that's the girlboss energy. 💅

🌸 SYNOPSIS 🌸

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

🦋 DESCRIPTION 🦋

Kalign (3.3.4). iconic, no notes. 🎀

✨ OPTIONS ✨

  • --format — Output format. Default is [Fasta] 💖
  • --type — Alignment type (rna, dna, internal). Default is [rna]. Options: protein, divergent (protein); rna, dna, internal (nuc). pick your fighter ✨
  • --gpo — Gap open penalty. Default is [] (yes, literally empty, no cap)
  • --gpe — Gap extension penalty. Default is []
  • --tgpe — Terminal gap extension penalty. Default is []
  • -n, --nthreads — Number of threads. Default is [4] 🧚
  • --version (-V / -v) — Prints version. Default is [NA]

🌈 EXAMPLES 🌈

Passing sequences via stdin:

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

Combining multiple input files:

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

Copyright © 2006,2019,2020,2021 Timo Lassmann

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.

⭐ Please cite: ⭐

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

and that's the whole page, bestie — written up as kalign 3.3.4, dated November 2022, filed under KALIGN(1). go align something gorgeous 💖✨🎀

📦 where this page comes from