---
name: "jaligner"
section: "1"
platform: "linux"
package: "jaligner"
version: "1.0+dfsg-11"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/jaligner"
---

# jaligner(1)

Smith-Waterman algorithm with Gotoh's improvement

## NAME

jaligner - Smith-Waterman algorithm with Gotoh's improvement

## SYNOPSIS

`jaligner` \<s1\> \<s2\> \<matrix\> \<open\> \<extend\>

Or just type `jaligner` to see the GUI.

## EXAMPLES

`jaligner` p53\_{human,mouse}.fasta BLOSUM62 10 0.5

## HOMEPAGE

 \<http://jaligner.sourceforge.net/\>