---
name: "kogalign.pl"
section: "1"
platform: "linux"
package: "murasaki-common"
version: "1.68.6-14"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kogalign.pl"
---

# kogalign.pl(1)

## NAME

kogalign.pl -- produce (untested) alignments from cds files

## SYNOPSIS

kogalign.pl --kogfile \<kogdata\> \<output\> \<input1\> \<input2\> \[\<input3\> ...\] kogalign.pl --kogfile \<kogdata\> \<alignment.seq\>

## OPTIONS The kogalign.pl \<aligment.seq\> execution style writes results to align.kogaligned

The --kogfile option is necessary.