eggNOG v7: phylogeny-based orthology predictions and functional annotations

[Data availability] All data are available through web queries and as bulk downloads at https://eggnogdb.org. Downloadable files include multiple sequence alignments and phylogenetic trees for all protein families, OG information, and functional annotation datasets.

Detalhes bibliográficos
Autores: Hernández-Plaza, Ana, Deng, Ziqi, Robledo-Yagüe, Fabian, Szklarczyk, Damian, Mering, Christian von, Bork, Peer, Huerta-Cepas, Jaime
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2026
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/419736
Acesso em linha:http://hdl.handle.net/10261/419736
https://api.elsevier.com/content/abstract/scopus_id/105027789612
Access Level:acceso abierto
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spelling eggNOG v7: phylogeny-based orthology predictions and functional annotationsHernández-Plaza, AnaDeng, ZiqiRobledo-Yagüe, FabianSzklarczyk, DamianMering, Christian vonBork, PeerHuerta-Cepas, Jaime[Data availability] All data are available through web queries and as bulk downloads at https://eggnogdb.org. Downloadable files include multiple sequence alignments and phylogenetic trees for all protein families, OG information, and functional annotation datasets.The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database is a phylogenomic resource for orthology inference, evolutionary analysis, and functional annotation across eukaryotes, bacteria, and archaea. Previous versions relied on best reciprocal hit triangulation and clustering approaches, which, although effective, faced challenges with the computational demands of large datasets, inconsistent hierarchical orthologous group (OG) reconstruction, and inaccurate classification of multidomain proteins. Here, we present eggNOG v7, the first release implementing a fully phylogenetic, domain-centric workflow. In this pipeline, sequences are first pre-clustered by Pfam domains or de novo clustering, followed by large-scale multiple sequence alignment and phylogenetic tree inference. Speciation and duplication events are then detected using a noise-tolerant algorithm to generate hierarchically consistent, evolutionarily dated OGs. Applied to 59.3 million proteins from 12 535 species, eggNOG v7 produced 3.18 million OGs, reducing singletons, fragmentation, and oversized groups compared to prior versions. Benchmarking against manually curated KEGG functional OGs demonstrated higher functional consistency. Additionally, eggNOG v7 provides updated protein functional annotations and a fully redesigned web interface with protein-centric searches, interactive phylogenies, and functional profiling tools. eggNOG v7 is available at https://eggnogdb.org.This study received support by grant PID2021-127210NB-I00 MCIU/AEI/FEDER, UE, National Programme for Fostering Excellence in Scientific and Technical Research; by the Spanish National Research Council (CSIC) grant INFRA24018; by CZI grant [DAF2020-218584] from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989). Cloud computing is supported by BMBF (de.NBI network #031A537B). Funding to pay the Open Access publication charges for this article was provided by the institutional funding.Peer reviewedOxford University PressEuropean CommissionAgencia Estatal de Investigación (España)Ministerio de Ciencia e Innovación (España)Consejo Superior de Investigaciones Científicas (España)Chan Zuckerberg InitiativeSilicon Valley Community FoundationFederal Ministry of Education and Research (Germany)Ministerio de Ciencia, Innovación y Universidades (España)Hernández-Plaza, Ana [0000-0002-9844-7999]Deng, Ziqi 0000-0001-5347-3846]Huerta-Cepas, Jaime [0000-0003-4195-5025]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262026info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/419736https://api.elsevier.com/content/abstract/scopus_id/105027789612reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-127210NB-I00The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1093/nar/gkaf1249https://doi.org/10.1093/nar/gkaf1249Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/4197362026-05-22T06:33:51Z
dc.title.none.fl_str_mv eggNOG v7: phylogeny-based orthology predictions and functional annotations
title eggNOG v7: phylogeny-based orthology predictions and functional annotations
spellingShingle eggNOG v7: phylogeny-based orthology predictions and functional annotations
Hernández-Plaza, Ana
title_short eggNOG v7: phylogeny-based orthology predictions and functional annotations
title_full eggNOG v7: phylogeny-based orthology predictions and functional annotations
title_fullStr eggNOG v7: phylogeny-based orthology predictions and functional annotations
title_full_unstemmed eggNOG v7: phylogeny-based orthology predictions and functional annotations
title_sort eggNOG v7: phylogeny-based orthology predictions and functional annotations
dc.creator.none.fl_str_mv Hernández-Plaza, Ana
Deng, Ziqi
Robledo-Yagüe, Fabian
Szklarczyk, Damian
Mering, Christian von
Bork, Peer
Huerta-Cepas, Jaime
author Hernández-Plaza, Ana
author_facet Hernández-Plaza, Ana
Deng, Ziqi
Robledo-Yagüe, Fabian
Szklarczyk, Damian
Mering, Christian von
Bork, Peer
Huerta-Cepas, Jaime
author_role author
author2 Deng, Ziqi
Robledo-Yagüe, Fabian
Szklarczyk, Damian
Mering, Christian von
Bork, Peer
Huerta-Cepas, Jaime
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Agencia Estatal de Investigación (España)
Ministerio de Ciencia e Innovación (España)
Consejo Superior de Investigaciones Científicas (España)
Chan Zuckerberg Initiative
Silicon Valley Community Foundation
Federal Ministry of Education and Research (Germany)
Ministerio de Ciencia, Innovación y Universidades (España)
Hernández-Plaza, Ana [0000-0002-9844-7999]
Deng, Ziqi 0000-0001-5347-3846]
Huerta-Cepas, Jaime [0000-0003-4195-5025]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description [Data availability] All data are available through web queries and as bulk downloads at https://eggnogdb.org. Downloadable files include multiple sequence alignments and phylogenetic trees for all protein families, OG information, and functional annotation datasets.
publishDate 2026
dc.date.none.fl_str_mv 2026
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/419736
https://api.elsevier.com/content/abstract/scopus_id/105027789612
url http://hdl.handle.net/10261/419736
https://api.elsevier.com/content/abstract/scopus_id/105027789612
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-127210NB-I00
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1093/nar/gkaf1249
https://doi.org/10.1093/nar/gkaf1249
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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