CheckAMG

Automated discovery and curation of Auxiliary Metabolic Genes (AMGs), Auxiliary Regulatory Genes (AReGs), and Auxiliary Physiology Genes (APGs) encoded by viral genomes

This tool is in active development and has not yet been peer-reviewed.

CheckAMG identifies and curates high-confidence auxiliary viral genes (AVGs) using two complementary approaches: an annotation-based path (curated functional annotations plus viral genome context) and a annotation-independent path (the Protein Set Transformer genome language model).

Quick usage

checkamg download -d /path/to/db/destination

checkamg end-to-end \
  -d /path/to/db/destination \
  -i examples/example_data/single_contig_viruses.fasta \
  -I examples/example_data/multi_contig_vMAGs \
  -o CheckAMG_example_out

Features

Input: nucleotide or protein sequences
Handles single-contig viral genomes and multi-contig vMAGs/bins
Reference-based annotation and genome-context curation (annotate)
Reference-independent prediction with a protein genome language model (de-novo)
Combined reporting (aggregate) and one-command runs (end-to-end)
Outputs curated lists and amino-acid sequences of AMGs, AReGs, and APGs

Modules

checkamg -h

download: get the required databases
annotate: reference-based AVG prediction and curation
de-novo: reference-independent AVG prediction with PST
aggregate: merge annotate and de-novo results
end-to-end: run annotate, de-novo, and aggregate in tandem
train: finetune a custom CheckAMG-PST model

License

GPL-3.0-or-later

Installation, example data, and full documentation: https://github.com/AnantharamanLab/CheckAMG and the CheckAMG Wiki.

Metadata

Release files for checkamg 1.1.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for checkamg 1.1.1
File	Size	Uploaded
checkamg-1.1.1.tar.gz	13.9 MB	Aug 3, 2026	Details

Release files / checkamg-1.1.1.tar.gz

Download URL	checkamg-1.1.1.tar.gz
Size	13.9 MB
Tags	Source
SHA-256 checksum How to use checksums	`d188884a33ba42b454156e66d887bbfb2219b2e1f018a3800e4e7c078ea65db4`
BLAKE2b-256 checksum How to use checksums	`246901aa862b37d07452fa788e0c6c6cfcdebde5bd62efdbe8f357210430f0d6`
Upload date	Aug 3, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.11.3`