# Install augustus with Homebrew, apt, Nix, pacman Predict genes in eukaryotic genomic sequences. Version 3.5.0 via Homebrew; verified 2026-06-25. ## Install ```sh sudo av install brew:augustus ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install augustus ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install augustus ``` Evidence: Debian stable package indexes: augustus from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#augustus ``` Evidence: nixpkgs package indexes: pkgs/by-name/au/augustus/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - pacman (92%): ```sh sudo pacman -S augustus ``` Evidence: Arch Linux sync databases: augustus from https://geo.mirror.pkgbuild.com/extra/os/x86_64/extra.db.tar.gz ## Package facts - **Package key:** brew:augustus - **Package manager:** Homebrew - **Package manager page:** - **Version:** 3.5.0 - **Source summary:** Predict genes in eukaryotic genomic sequences - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** Artistic-1.0 - **Source archive:** - **Last updated:** 2026-06-25T13:37:37+02:00 - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - aln2wig (cli) - augustus (cli) - bam2hints (cli) - bam2wig (cli) - compileSpliceCands (cli) - etraining (cli) - fastBlockSearch (cli) - filterBam (cli) - homGeneMapping (cli) - joingenes (cli) - pp_simScore (cli) - prepareAlign (cli) - aln2wig (alias) - augustus (alias) - bam2hints (alias) - bam2wig (alias) - compileSpliceCands (alias) - etraining (alias) - fastBlockSearch (alias) - filterBam (alias) - homGeneMapping (alias) - joingenes (alias) - pp_simScore (alias) - prepareAlign (alias) ## Dependencies - bamtools - boost - htslib ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 3.5.0 - Package-manager updated: 2026-06-25 - Local data: ok - Upstream repository: https://github.com/Gaius-Augustus/Augustus - Upstream latest detected: v3.5.0 (current) ## Project history and usage AUGUSTUS is a gene prediction system for eukaryotic genomic sequences. In package-manager terms it is a bioinformatics CLI suite with a large config/species data payload, training parameters, auxiliary tools, and workflows that bridge local command-line runs, web services, and genome annotation pipelines. ### Project history The University of Greifswald project site identifies AUGUSTUS as a program for predicting genes in eukaryotic genomic sequences and carries 2003 metadata. The official reference list traces the research lineage from Mario Stanke's 2003 hidden-Markov-model work through the 2004 AUGUSTUS web-server paper and later papers on hints, alternative transcripts, cDNA alignments, and comparative gene prediction. The current GitHub README says AUGUSTUS can find genes and gene structures in one or more genomes, can run ab initio, and can incorporate hints from EST, protein alignments, MS/MS, and syntenic genomic alignments. The ABOUT document notes that since version 3.0 it can predict genes simultaneously in several aligned genomes. The project site records several adoption-era milestones: an automatic annotation pipeline was distributed by 2009, RNA-Seq integration was documented in 2012, and source-code issue handling moved to GitHub. Releases on GitHub include 3.3.2 in 2018, 3.3.3 in 2019, 3.4.0 in 2020, and 3.5.0 in 2022. ### Adoption history AUGUSTUS adoption is driven by genome annotation workflows rather than casual CLI use. The official site offers web interfaces, a larger WebAUGUSTUS service, local downloads, training, species parameter sets, and links to accuracy results. The supplied package-manager facts show Homebrew, Debian, Nix, Arch, and Ubuntu packages, reflecting its role as a reproducible command-line dependency in bioinformatics environments. ### How it is used The official running guide describes the basic command as augustus [parameters] --species=SPECIES queryfilename, with uncompressed FASTA input and GTF-like output. Users choose species parameter sets, redirect output to GFF/GTF files, pass hints files and extrinsic configuration, retrain species parameters, and run auxiliary programs such as etraining and bam2hints. ### Why package nerds care AUGUSTUS is package-interesting because the executable alone is not enough: the config directory, species parameters, extrinsic.cfg, scripts, examples, and auxiliary programs must line up with AUGUSTUS_CONFIG_PATH or the executable-relative ../config fallback. It is a classic scientific package where data files, environment variables, and compiled tools are one deployable unit. ### Timeline - 2003: Foundational HMM gene-prediction thesis and related Bioinformatics paper appeared. - 2004: AUGUSTUS web-server paper was published. - 2006: Papers covered alternative transcripts and extrinsic hints. - 2008: cDNA and syntenic alignment improvements were published. - 2009: The project site announced an automatic annotation pipeline for download. - 2012: RNA-Seq integration for the download version was documented. - 2016: Multi-genome gene finding was published. - 2018: GitHub release 3.3.2 was published. - 2022: GitHub release 3.5.0 was published. ### Related projects - AUGUSTUS is commonly discussed with WebAUGUSTUS, BRAKER, comparative gene prediction workflows, RNA-Seq hint generation, genome browsers such as Gbrowse, and the broader University of Greifswald bioinformatics toolchain. ### Sources - - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Configuration and credential file locations These source-backed paths show where this package keeps local settings or durable credentials. Automic Vault can use them as review targets for secret scanning, migration, and command approval. ## Configuration files - Unix: $AUGUSTUS_CONFIG_PATH, ../config relative to the augustus executable, $AUGUSTUS_CONFIG_PATH/extrinsic/extrinsic.cfg ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** augustus - **Version Scheme:** 0 - **Revision:** 12 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Other Package-Manager Records - Debian apt - augustus - 3.5.0+dfsg-5: normalized package name match | Debian stable package indexes: augustus from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | gene prediction in eukaryotic genomes | https://bioinf.uni-greifswald.de/augustus/ - Debian apt - augustus-data - 3.5.0+dfsg-5: normalized package name match | Debian stable package indexes: augustus-data from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | data files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/ - Debian apt - augustus-doc - 3.5.0+dfsg-5: normalized package name match | Debian stable package indexes: augustus-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | documentation files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/ - Nix - augustus: normalized package name match | nixpkgs package indexes: pkgs/by-name/au/augustus/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - augustus - 3.5.0+dfsg-4build5: normalized package name match | Ubuntu 24.04 LTS package indexes: augustus from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | gene prediction in eukaryotic genomes | https://bioinf.uni-greifswald.de/augustus/ - Ubuntu apt - augustus-data - 3.5.0+dfsg-4build5: normalized package name match | Ubuntu 24.04 LTS package indexes: augustus-data from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | data files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/ - Ubuntu apt - augustus-doc - 3.5.0+dfsg-4build5: normalized package name match | Ubuntu 24.04 LTS package indexes: augustus-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | documentation files for AUGUSTUS | https://bioinf.uni-greifswald.de/augustus/ - pacman - augustus - 4.0.0-2: normalized package name match | Arch Linux sync databases: augustus from https://geo.mirror.pkgbuild.com/extra/os/x86_64/extra.db.tar.gz | An enhanced re-implementation of Caesar III | https://github.com/Keriew/augustus ## Related links - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [Homebrew utility packages](https://www.automicvault.com/pkg/brew-utility-packages/) - Matched Homebrew package provider. - [bamtools](https://www.automicvault.com/pkg/brew/bamtools/) - Runtime dependency declared by Homebrew. - [htslib](https://www.automicvault.com/pkg/brew/htslib/) - Runtime dependency declared by Homebrew. - [prodigal](https://www.automicvault.com/pkg/brew/prodigal/) - Shares av.db curated category or tags: bioinformatics, cli, gene-prediction, science. - [abpoa](https://www.automicvault.com/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abyss](https://www.automicvault.com/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [any2fasta](https://www.automicvault.com/pkg/brew/any2fasta/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [autocycler](https://www.automicvault.com/pkg/brew/autocycler/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [bcftools](https://www.automicvault.com/pkg/brew/bcftools/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, htslib, science. - [freebayes](https://www.automicvault.com/pkg/brew/freebayes/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, htslib, science. ## Combined YAML source View the package source record on GitHub. [combined/augustus.yml](https://github.com/automic-vault/db/blob/main/combined/augustus.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated configuration and credential file locations - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph