---
name: "gapcleaner"
section: "1"
platform: "linux"
package: "fsa"
version: "1.15.9+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gapcleaner"
---

# gapcleaner(1)

Find the most-parsimonious ordering of indels

## NAME

gapcleaner - Find the most-parsimonious ordering of indels

## SYNOPSIS

**gapcleaner** *\<multi-FASTA or Stockholm alignment\>*

## DESCRIPTION

gapcleaner from FSA 1.15.9

Find the most-parsimonious ordering of indels. Finds the minimal chain decomposition of the POSET of the alignment; this corresponds to minimizing the number of gap-openings across the sequences.

Input protein alignment must be in multi-FASTA or Stockholm format.

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.