{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T23:27:50Z","timestamp":1786663670328,"version":"build-2736575974"},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T00:00:00Z","timestamp":1780963200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":66,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32060003"],"award-info":[{"award-number":["32060003"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/s12859-026-06506-z","type":"journal-article","created":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T10:23:44Z","timestamp":1781000624000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["LSGFA: domain-based infraspecific large-scale prokaryotic genomic orthologous gene inference"],"prefix":"10.1186","volume":"27","author":[{"given":"Yu","family":"Zhao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Fei","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuan","family":"Hai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Yang","family":"Zhi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,9]]},"reference":[{"key":"6506_CR1","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1038\/s41576-020-0233-0","volume":"21","author":"P Kapli","year":"2020","unstructured":"Kapli P, Yang Z, Telford MJ. Phylogenetic tree building in the genomic age. Nat Rev Genet. 2020;21:428\u201344.","journal-title":"Nat Rev Genet"},{"key":"6506_CR2","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1093\/bib\/bbr030","volume":"12","author":"DM Kristensen","year":"2011","unstructured":"Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. Computational methods for gene orthology inference. Brief Bioinform. 2011;12:379\u201391.","journal-title":"Brief Bioinform"},{"key":"6506_CR3","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","volume":"13","author":"L Li","year":"2003","unstructured":"Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178\u201389.","journal-title":"Genome Res"},{"key":"6506_CR4","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:238.","journal-title":"Genome Biol"},{"key":"6506_CR5","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691\u20133.","journal-title":"Bioinformatics"},{"key":"6506_CR6","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1137\/040608635","volume":"30","author":"S Van Dongen","year":"2008","unstructured":"Van Dongen S. Graph clustering via a discrete uncoupling process. SIAM J Matrix Anal Appl. 2008;30:121\u201341.","journal-title":"SIAM J Matrix Anal Appl"},{"key":"6506_CR7","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1186\/s13059-024-03362-z","volume":"25","author":"DQ Le","year":"2024","unstructured":"Le DQ, Nguyen TA, Nguyen SH, Nguyen TT, Nguyen CH, Phung HT, et al. Efficient inference of large prokaryotic pangenomes with PanTA. Genome Biol. 2024;25:209.","journal-title":"Genome Biol"},{"key":"6506_CR8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-020-02090-4","volume":"21","author":"G Tonkin-Hill","year":"2020","unstructured":"Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol. 2020;21:1\u201321.","journal-title":"Genome Biol"},{"key":"6506_CR9","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03298-4","volume":"25","author":"S Cosentino","year":"2024","unstructured":"Cosentino S, Sriswasdi S, Iwasaki W. SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models. Genome Biol. 2024;25:195.","journal-title":"Genome Biol"},{"key":"6506_CR10","doi-asserted-by":"publisher","first-page":"9865","DOI":"10.1038\/s41467-025-64846-5","volume":"16","author":"C Bu","year":"2025","unstructured":"Bu C, Zhang H, Zhang F, Liang W, Gao H, Zhao J, et al. PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks. Nat Commun. 2025;16:9865.","journal-title":"Nat Commun"},{"key":"6506_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-41695-z","volume":"9","author":"VA Traag","year":"2019","unstructured":"Traag VA, Waltman L, van Eck NJ. From Louvain to Leiden: guaranteeing well-connected communities. Sci Rep. 2019;9:5233.","journal-title":"Sci Rep"},{"key":"6506_CR12","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18:366\u20138.","journal-title":"Nat Methods"},{"key":"6506_CR13","doi-asserted-by":"publisher","first-page":"2856","DOI":"10.1093\/bioinformatics\/bty1057","volume":"35","author":"M Mirdita","year":"2019","unstructured":"Mirdita M, Steinegger M, S\u00f6ding J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics. 2019;35:2856\u20138.","journal-title":"Bioinformatics"},{"key":"6506_CR14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002195","volume":"7","author":"SR Eddy","year":"2011","unstructured":"Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7:e1002195.","journal-title":"PLoS Comput Biol"},{"key":"6506_CR15","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068\u20139.","journal-title":"Bioinformatics"},{"key":"6506_CR16","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/BF01908075","volume":"2","author":"L Hubert","year":"1985","unstructured":"Hubert L, Arabie P. Comparing partitions. J Classif. 1985;2:193\u2013218.","journal-title":"J Classif"},{"key":"6506_CR17","doi-asserted-by":"publisher","first-page":"2444","DOI":"10.1093\/molbev\/msl117","volume":"23","author":"M Wang","year":"2006","unstructured":"Wang M, Caetano-Anoll\u00e9s G. Global phylogeny determined by the combination of protein domains in proteomes. Mol Biol Evol. 2006;23:2444\u201354.","journal-title":"Mol Biol Evol"},{"key":"6506_CR18","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1140\/epjb\/e2007-00088-4","volume":"56","author":"JM Kumpula","year":"2007","unstructured":"Kumpula JM, Saram\u00e4ki J, Kaski K, Kert\u00e9sz J. Limited resolution in complex network community detection with Potts model approach. Eur Phys J B. 2007;56:41\u20135.","journal-title":"Eur Phys J B"},{"key":"6506_CR19","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1073\/pnas.0605965104","volume":"104","author":"S Fortunato","year":"2007","unstructured":"Fortunato S, Barth\u00e9lemy M. Resolution limit in community detection. Proc Natl Acad Sci USA. 2007;104:36\u201341.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6506_CR20","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-3137-2","volume":"20","author":"E Persson","year":"2019","unstructured":"Persson E, Kaduk M, Forslund SK, Sonnhammer ELL. Domainoid: domain-oriented orthology inference. BMC Bioinformatics. 2019;20:523.","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-026-06506-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-026-06506-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-026-06506-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T22:52:51Z","timestamp":1786661571000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12859-026-06506-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,9]]},"references-count":20,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["6506"],"URL":"https:\/\/doi.org\/10.1186\/s12859-026-06506-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,9]]},"assertion":[{"value":"11 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing Interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"178"}}