---
name: "augustus"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/augustus"
---

# augustus(1)

a gene prediction tool

## NAME

augustus - a gene prediction tool

## SYNOPSIS

**augustus** \[parameters\] --species=SPECIES queryfilename

## OPTIONS

The mandatory option 'queryfilename' specifies the filename (including relative path) to the file containing the query sequence(s) in FASTA format.

SPECIES is an identifier for the species. Use **--species=help** to see a list.

### Further parameters:

- **--strand=both**, **--strand=forward** or **--strand=backward**

  define the strand to search on

- **--genemodel=genemodel**

  where genemodel is one of:

  • partial      - allow prediction of incomplete genes at the sequence boundaries (default)

  • intronless   - only predict single-exon genes like in prokaryotes and some eukaryotes

  • complete     - only predict complete genes

  • atleastone   - predict at least one complete gene

  • exactlyone   - predict exactly one complete gene

- **--singlestrand=true**

  predict genes independently on each strand, allow overlapping genes on opposite strands. This option is turned off by default.

- **--hintsfile=hintsfilename**

  When this option is used the prediction considering hints (extrinsic information) is turned on. hintsfilename contains the hints in gff format.

- **--AUGUSTUS\_CONFIG\_PATH=path**

  path to config directory (if not specified as environment variable)

- **--alternatives-from-evidence=true/false**

  report alternative transcripts when they are suggested by hints

- **--alternatives-from-sampling=true/false**

  report alternative transcripts generated through probabilistic sampling

- **--maxtracks=n**

  For a description of these parameters see section "SAMPLING: ALTERNATIVE TRANSCRIPTS AND POSTERIOR PROBABILITIES" of docs/RUNNING-AUGUSTUS.md.

- **--proteinprofile=filename**

  When this option is used the prediction will consider the protein profile provided as parameter. The protein profile extension is described in section "AUGUSTUS-PPX" of docs/RUNNING-AUGUSTUS.md.

- **--progress=true**

  show a progressmeter

- **--gff3=on/off**

  output in gff3 format

- **--predictionStart=A**, **--predictionEnd=B**

  A and B define the range of the sequence for which predictions should be found.

- **--UTR=on/off**

  predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.

- **--noInFrameStop=true/false**

  Do not report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur. Default: false

- **--noprediction=true/false**

  If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.

- **--uniqueGeneId=true/false**

  If true, output gene identifyers like this: seqname.gN

- **--paramlist**

  Show full list of supported parameters.

## AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

## ADDITIONAL DOCUMENTATION

An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.