---
name: "ali2gff"
section: "1"
platform: "linux"
package: "gff2aplot"
version: "2.0-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ali2gff"
---

# ali2gff(1)

Module to translate a MUMmer output files into gff formatted output.

## NAME

ali2gff - Module to translate a MUMmer output files into gff formatted output.

## SYNOPSIS

**ali2gff** \[-r\] \[-t \<.\|0\|1\|2\>\] \[-x \<name\>\] \[-y \<name\>\] \[-H\] \[-f\] \[-h\] \<MUMmer\_output\_file\>\

## OPTIONS

- **-h, --help**

  Show summary of options.

- **-r**

  Interchange the order of sequences (sequence 1 on y-axis, sequence 2 on x-axis).

- **-t \<.\|0\|1\|2\>**

  Put label 'frame' in gff output.

- **-x \<name\>**

  Specify the species name for species1 (default: "Seq1").

- **-y \<name\>**

  Specify the species name for species2 (default: "Seq2").

- **-i**

  Ignore full sequence identities.

- **-f**

  Write output to file.

## SEE ALSO

[**blat2gff**(1)](/blat2gff/1.md), [**gff2aplot**(1)](/gff2aplot/1.md), [**parseblast**(1)](/parseblast/1.md), [**sim2gff**(1)](/sim2gff/1.md).\

## AUTHOR

ali2gff was written by Steffi Gebauer-Jung.

This manual page was written by Nelson A. de Oliveira \<naoliv@gmail.com\>, for the Debian project (but may be used by others).