{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T03:04:54Z","timestamp":1777518294809,"version":"3.51.4"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"suppl_1","license":[{"start":{"date-parts":[[2017,5,10]],"date-time":"2017-05-10T00:00:00Z","timestamp":1494374400000},"content-version":"vor","delay-in-days":2741,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1]]},"DOI":"10.1093\/nar\/gkp951","type":"journal-article","created":{"date-parts":[[2009,11,10]],"date-time":"2009-11-10T01:25:20Z","timestamp":1257816320000},"page":"D190-D195","source":"Crossref","is-referenced-by-count":191,"title":["eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations"],"prefix":"10.1093","volume":"38","author":[{"given":"J.","family":"Muller","sequence":"first","affiliation":[]},{"given":"D.","family":"Szklarczyk","sequence":"additional","affiliation":[]},{"given":"P.","family":"Julien","sequence":"additional","affiliation":[]},{"given":"I.","family":"Letunic","sequence":"additional","affiliation":[]},{"given":"A.","family":"Roth","sequence":"additional","affiliation":[]},{"given":"M.","family":"Kuhn","sequence":"additional","affiliation":[]},{"given":"S.","family":"Powell","sequence":"additional","affiliation":[]},{"given":"C.","family":"von Mering","sequence":"additional","affiliation":[]},{"given":"T.","family":"Doerks","sequence":"additional","affiliation":[]},{"given":"L. J.","family":"Jensen","sequence":"additional","affiliation":[]},{"given":"P.","family":"Bork","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2009,11,7]]},"reference":[{"key":"key\n\t\t\t\t20170408060539_B1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins","volume":"19","author":"Fitch","year":"1970","journal-title":"Syst. Zool."},{"key":"key\n\t\t\t\t20170408060539_B2","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families","volume":"278","author":"Tatusov","year":"1997","journal-title":"Science"},{"key":"key\n\t\t\t\t20170408060539_B3","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev.genet.39.073003.114725","article-title":"Orthologs, paralogs, and evolutionary genomics","volume":"39","author":"Koonin","year":"2005","journal-title":"Annu. Rev. Genet."},{"key":"key\n\t\t\t\t20170408060539_B4","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/S0168-9525(02)02793-2","article-title":"Orthology, paralogy and proposed classification for paralog subtypes","volume":"18","author":"Sonnhammer","year":"2002","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20170408060539_B5","doi-asserted-by":"crossref","first-page":"D263","DOI":"10.1093\/nar\/gkm1020","article-title":"InParanoid 6: eukaryotic ortholog clusters with inparalogs","volume":"36","author":"Berglund","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B6","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170408060539_B7","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1745-6150-2-33","article-title":"Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea","volume":"2","author":"Makarova","year":"2007","journal-title":"Biol. Direct."},{"key":"key\n\t\t\t\t20170408060539_B8","doi-asserted-by":"crossref","first-page":"D271","DOI":"10.1093\/nar\/gkm845","article-title":"OrthoDB: the hierarchical catalog of eukaryotic orthologs","volume":"36","author":"Kriventseva","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B9","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1186\/1471-2105-9-518","article-title":"Algorithm of OMA for large-scale orthology inference","volume":"9","author":"Roth","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170408060539_B10","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170408060539_B11","first-page":"D343","article-title":"MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups","volume-title":"Nucleic Acids Res.","author":"Uchiyama","year":"2007"},{"key":"key\n\t\t\t\t20170408060539_B12","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/1471-2105-8-83","article-title":"Orthology prediction at scalable resolution by phylogenetic tree analysis","volume":"8","author":"van der Heijden","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170408060539_B13","doi-asserted-by":"crossref","first-page":"i549","DOI":"10.1093\/bioinformatics\/btm193","article-title":"Automatic genome-wide reconstruction of phylogenetic gene trees","volume":"23","author":"Wapinski","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170408060539_B14","doi-asserted-by":"crossref","first-page":"D491","DOI":"10.1093\/nar\/gkm899","article-title":"PhylomeDB: a database for genome-wide collections of gene phylogenies","volume":"36","author":"Huerta-Cepas","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B15","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1101\/gr.073585.107","article-title":"EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates","volume":"19","author":"Vilella","year":"2009","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170408060539_B16","first-page":"W84","article-title":"Berkeley PHOG: PhyloFacts orthology group prediction web server","volume-title":"Nucleic Acids Res.","author":"Datta","year":"2009"},{"key":"key\n\t\t\t\t20170408060539_B17","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/bib\/bbl030","article-title":"HCOP: a searchable database of human orthology predictions","volume":"8","author":"Eyre","year":"2007","journal-title":"Brief Bioinform."},{"key":"key\n\t\t\t\t20170408060539_B18","doi-asserted-by":"crossref","first-page":"W428","DOI":"10.1093\/nar\/gkp462","article-title":"ProGMap: an integrated annotation resource for protein orthology","volume":"37","author":"Kuzniar","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B19","doi-asserted-by":"crossref","first-page":"D250","DOI":"10.1093\/nar\/gkm796","article-title":"eggNOG: automated construction and annotation of orthologous groups of genes","volume":"36","author":"Jensen","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B20","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"35","author":"Pruitt","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B21","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkn828","article-title":"Ensembl 2009","volume":"37","author":"Hubbard","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B22","doi-asserted-by":"crossref","first-page":"D526","DOI":"10.1093\/nar\/gkn631","article-title":"GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis","volume":"37","author":"Aurrecoechea","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B23","doi-asserted-by":"crossref","first-page":"D1009","DOI":"10.1093\/nar\/gkm965","article-title":"The Arabidopsis Information Resource (TAIR): gene structure and function annotation","volume":"36","author":"Swarbreck","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B24","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkn760","article-title":"STRING 8\u2013a global view on proteins and their functional interactions in 630 organisms","volume":"37","author":"Jensen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B25","doi-asserted-by":"crossref","first-page":"D684","DOI":"10.1093\/nar\/gkm795","article-title":"STITCH: interaction networks of chemicals and proteins","volume":"36","author":"Kuhn","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B26","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B27","doi-asserted-by":"crossref","first-page":"W535","DOI":"10.1093\/nar\/gki423","article-title":"PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology","volume":"33","author":"Saebo","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B28","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"Kanehisa","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B29","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The Gene Ontology (GO) database and informatics resource","volume":"32","author":"Harris","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B30","doi-asserted-by":"crossref","first-page":"D229","DOI":"10.1093\/nar\/gkn808","article-title":"SMART 6: recent updates and new developments","volume":"37","author":"Letunic","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B31","doi-asserted-by":"crossref","first-page":"D281","DOI":"10.1093\/nar\/gkm960","article-title":"The Pfam protein families database","volume":"36","author":"Finn","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B32","doi-asserted-by":"crossref","first-page":"D169","DOI":"10.1093\/nar\/gkn664","article-title":"The Universal Protein Resource (UniProt)","volume":"37","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B33","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B34","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060539_B35","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1093\/bib\/bbn013","article-title":"Recent developments in the MAFFT multiple sequence alignment program","volume":"9","author":"Katoh","year":"2008","journal-title":"Brief Bioinform."},{"key":"key\n\t\t\t\t20170408060539_B36","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1126\/science.1158395","article-title":"Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis","volume":"320","author":"Loytynoja","year":"2008","journal-title":"Science"},{"key":"key\n\t\t\t\t20170408060539_B37","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1002\/prot.20527","article-title":"BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark","volume":"61","author":"Thompson","year":"2005","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170408060539_B38","first-page":"164","article-title":"PHYLIP \u2013 Phylogeny Inference Package (Version 3.2)","volume":"5","author":"Felsenstein","year":"1989","journal-title":"Cladistics"},{"key":"key\n\t\t\t\t20170408060539_B39","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"Guindon","year":"2003","journal-title":"Syst. Biol."},{"key":"key\n\t\t\t\t20170408060539_B40","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bia01es00","article-title":"Sequence file format conversion with command-line readseq","volume-title":"Curr. Protoc. Bioinformatics","author":"Gilbert","year":"2003"},{"key":"key\n\t\t\t\t20170408060539_B41","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2013a multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170408060539_B42","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170408060539_B43","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1093\/bioinformatics\/17.4.383","article-title":"ATV: display and manipulation of annotated phylogenetic trees","volume":"17","author":"Zmasek","year":"2001","journal-title":"Bioinformatics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/38\/suppl_1\/D190\/11218238\/gkp951.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:41:10Z","timestamp":1522680070000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkp951"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,11,7]]},"references-count":43,"journal-issue":{"issue":"suppl_1","published-online":{"date-parts":[[2009,11,7]]},"published-print":{"date-parts":[[2010,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkp951","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,11,7]]}}}