Augustus  3.5.0
About: AUGUSTUS is a program to find genes and their structures in one or more genomes.
  Fossies Dox: Augustus-3.5.0.tar.gz  ("unofficial" and yet experimental doxygen-generated source code documentation)  

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Augustus Documentation

Some Fossies usage hints in advance:

  1. To see the Doxygen generated documentation please click on one of the items in the steelblue colored "quick index" bar above or use the side panel at the left which displays a hierarchical tree-like index structure and is adjustable in width.
  2. If you want to search for something by keyword rather than browse for it you can use the client side search facility (using Javascript and DHTML) that provides live searching, i.e. the search results are presented and adapted as you type in the Search input field at the top right.
  3. Doxygen doesn't incorporate all member files but just a definable subset (basically the main project source code files that are written in a supported language). So to search and browse all member files you may visit the Fossies Augustus-3.5.0.tar.gz contents page and use the Fossies standard member browsing features (also with source code highlighting and additionally with optional code folding).

Build and test

Gene Prediction with AUGUSTUS



AUGUSTUS is a program to find genes and their structures in one or more genomes. More ...



Windows users can use the Windows Subsystem for Linux (WSL) to install AUGUSTUS exactly as described below for Linux. How to set up the WSL for AUGUSTUS is described here.

Ubuntu 18.04, Debian 9 or later

Until Ubuntu 21.04 and Debian 11 only as single-genome version, since then with capability for comparative gene prediction.

sudo apt install augustus augustus-data augustus-doc


Create a docker image from Dockerfile using:

git clone
cd Augustus
docker build -t augustus .


Create a Singularity Image File from the Singularity Definition File using

git clone
cd Augustus
singularity build augustus.sif Singularity.def

Building AUGUSTUS from source

See for details.

Download source code from github and compile:

git clone
cd Augustus
make augustus

After compilation has finished, the command bin/augustus should be executable and print a usage message.

For utilities use

make auxprogs

Install locally

As a normal user, add the directory of the executables to the PATH environment variable, for example:

export PATH=~/augustus/bin:~/augustus/scripts:$PATH

Install globally

You can install AUGUSTUS globally, if you have root privileges, for example:

sudo make install

Alternatively, you can exectue similar commands to those in the "install" section of the top-level Makefile to customize the global installation.

Optional: set environment variable AUGUSTUS_CONFIG_PATH

If the environment variable AUGUSTUS_CONFIG_PATH is set, augustus and etraining will look there for the config directory that contains the configuration and parameter files, e.g. '~/augustus/config'. You may want to add this line to a startup script (like ~/.bashrc).

export AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/

If this environment variable is not set, then the programs will look in the path ../config relative to the directory in which the executable lies. As a third alternative, you can specify this directory on the command line when you run augustus: --AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/


AUGUSTUS can also be run through a web-interface at and a web service at


Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24(5), pages 637–644, doi: 10.1093/bioinformatics/btn013

For further references see docs/

3 book chapters with command line walkthroughs


All source code, i.e.

  • the AUGUSTUS source code (src/*.cc, include/*.hh)
  • the scripts (scripts/*)
  • the auxiliary programs (auxprogs/)
  • the tree-parser (src/scanner, src/parser)
  • the unit tests (src/unittests)

is under the Artistic License.