---
name: "kalign"
section: "1"
platform: "linux"
package: "kalign"
version: "1:3.4.0-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kalign"
---

# kalign(1)

Global and progressive multiple sequence alignment

## NAME

kalign - Global and progressive multiple sequence alignment

## SYNOPSIS

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

## DESCRIPTION

Kalign (3.3.4)

## OPTIONS

- **--format**

  : Output format. \[Fasta\]

- **--type**

  : Alignment type (rna, dna, internal). \[rna\] Options: protein, divergent (protein)

-

  rna, dna, internal (nuc).

- **--gpo**

  : Gap open penalty. \[\]

- **--gpe**

  : Gap extension penalty. \[\]

- **--tgpe**

  : Terminal gap extension penalty. \[\]

- **-n**/--nthreads

  : Number of threads. \[4\]

- **--version** (**-V**/-v)

  : Prints version. \[NA\]

## 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

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