eggNOG‑mapper3
Annotate Star 789 v3.0.0-beta6

Functional annotation at the metagenomic scale

eggNOG-mapper annotates large sequence sets — metagenomic protein catalogs, whole proteomes, CDS or prokaryotic contigs — adjusting the taxonomic context individually for every query, using eggNOG 7 orthologous groups and their gene trees.

Job queue live
18running
48queued
24submitters
196done · 24 h
•••@163.com proteins · 27,502 seqs 2h59m
SubmitterTypeSeqsStatus
Running18
•••@163.com proteins · v3 27,502 2h59mR
•••@163.com proteins · v3 21,311 2h51mR
•••@ump.edu.vn proteins · v3 34,701 2h29mR
•••@gmail.com proteins · v3 5,591 2h06mR
•••@qq.com proteins · v3 29,051 1h28mR
•••@helmholtz-hips.de genome · v3 208 1h18mR
•••@gmail.com proteins · v3 2,559 1h15mR
•••@163.com proteins · v3 91,575 1h04mR
•••@kth.se proteins · v3 6,040 42mR
•••@student.dongguk.edu CDS · v3 14 33mR
•••@goa.bits-pilani.ac.in proteins · v2 40,707 22mR
•••@gmail.com CDS · v3 6,802 14mR
•••@unibz.it proteins · v3 1,600 8mR
•••@gmail.com proteins · v3 514 7mR
•••@qq.com proteins · v3 43,908 7mR
•••@ice.mpg.de genome · v3 1 7mR
•••@cmu.ac.th proteins · v3 4,215 3mR
•••@unavarra.es proteins · v3 603 2mR
Queued48
•••@qq.com proteins · v3 30,132 3h59mQ
•••@helmholtz-hips.de genome · v3 1,203 3h21mQ
•••@helmholtz-hips.de genome · v3 3,145 3h20mQ
•••@helmholtz-hips.de genome · v3 1,107 3h20mQ
+ 44 more waiting in line
Recently finished
•••@unavarra.es proteins · v3 807 1h18mD
•••@cmu.ac.th proteins · v3 4,286 1h45mD
•••@ice.mpg.de genome · v3 5 1h24mD
•••@qq.com proteins · v3 57,023 3h48mD
•••@gmail.com proteins · v3 327 49mD
News & updates
  • Sep 2FixFixed jobs that could fail with a connection error (“socket is closed”).
  • Aug 15FixJob compute time is now reported correctly.
  • Aug 14FixFixed out-of-memory failures on large annotation jobs.
Earlier updates (1)
  • Aug 14FixFixed genome/contig jobs that could finish without producing output.

What's new in v3

eggNOG-mapper v3 rebuilds the annotation engine around eggNOG 7: a larger curated foundation (12,535 reference proteomes, 59.3M proteins, 3.18M orthologous groups), per-query taxonomic scoping, and a cascade transfer that keeps only the closest curated evidence.

eggNOG v7 database

A larger, curated orthology foundation: 12,535 reference proteomes — 10,756 Bacteria, 457 Archaea and 1,322 Eukaryota — with 59.3M proteins in 3.18M orthologous groups.

Curated-only donors

Functional terms are transferred only from manually reviewed sources — no electronically inferred annotations are propagated.

Updated functional sources

Terms are drawn from current releases of Swiss-Prot, KEGG, Gene Ontology, COG, PFAM and EC.

Per-seed taxonomic ceiling

The taxonomic scope is adjusted for every query, so mixed metagenomic communities annotate correctly without one global clade.

Cascade annotation engine

A lazy closest-cascade walks outward tier by tier and keeps the nearest evolutionary evidence available.

How to cite

If you use results from this service, please cite both the tool and the database.

Tool

Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2. Mol Biol Evol. 2021;38(12):5825–5829. doi:10.1093/molbev/msab293

Database

Hernández-Plaza A, Deng D, Robledo-Yagüe A, et al. eggNOG v7. Nucleic Acids Res. 2026;54(D1):D402–D408. doi:10.1093/nar/gkaf1249

Suggested citation format

Functional annotation was performed with eggNOG-mapper v3.0.0 (Cantalapiedra et al., 2021) using orthology assignments from the eggNOG 7 database (Hernández-Plaza et al., 2026). Homology searches used DIAMOND in sensitive mode (e-value ≤ 0.001), transferring GO, KEGG, COG and PFAM terms from orthologs within the automatically adjusted taxonomic scope (--tax_scope auto).

Source & support

Open source under AGPL-3.0. Report issues and ask questions on GitHub.

View on GitHub