{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T10:11:16Z","timestamp":1781604676105,"version":"3.54.5"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,5,12]],"date-time":"2023-05-12T00:00:00Z","timestamp":1683849600000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF0703703"],"award-info":[{"award-number":["2021YFF0703703"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFC0863300"],"award-info":[{"award-number":["2021YFC0863300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Collaborative Research Program of the Alliance of International Science Organizations","award":["ANSO-CR-KP-2022-09"],"award-info":[{"award-number":["ANSO-CR-KP-2022-09"]}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDB38060100"],"award-info":[{"award-number":["XDB38060100"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32270718"],"award-info":[{"award-number":["32270718"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170678"],"award-info":[{"award-number":["32170678"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Youth Innovation Promotion Association of CAS","award":["2017141"],"award-info":[{"award-number":["2017141"]}]},{"DOI":"10.13039\/501100005090","name":"Beijing Nova Program","doi-asserted-by":"publisher","award":["Z211100002121006"],"award-info":[{"award-number":["Z211100002121006"]}],"id":[{"id":"10.13039\/501100005090","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Haplotype networks are graphs used to represent evolutionary relationships between a set of taxa and are characterized by intuitiveness in analyzing genealogical relationships of closely related genomes. We here propose a novel algorithm termed McAN that considers mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time when constructing haplotype network. We show that McAN is two orders of magnitude faster than state-of-the-art algorithms without losing accuracy, making it suitable for analysis of a large number of sequences. Based on our algorithm, we developed an online web server and offline tool for haplotype network construction, community lineage determination, and interactive network visualization. We demonstrate that McAN is highly suitable for analyzing and visualizing massive genomic data and is helpful to enhance the understanding of genome evolution. Availability: Source code is written in C\/C++ and available at https:\/\/github.com\/Theory-Lun\/McAN and https:\/\/ngdc.cncb.ac.cn\/biocode\/tools\/BT007301 under the MIT license. Web server is available at https:\/\/ngdc.cncb.ac.cn\/bit\/hapnet\/. SARS-CoV-2 dataset are available at https:\/\/ngdc.cncb.ac.cn\/ncov\/. Contact: songshh@big.ac.cn (Song S), zhaowm@big.ac.cn (Zhao W), baoym@big.ac.cn (Bao Y), zhangzhang@big.ac.cn (Zhang Z), ybxue@big.ac.cn (Xue Y).<\/jats:p>","DOI":"10.1093\/bib\/bbad174","type":"journal-article","created":{"date-parts":[[2023,5,12]],"date-time":"2023-05-12T08:02:27Z","timestamp":1683878547000},"source":"Crossref","is-referenced-by-count":9,"title":["McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks"],"prefix":"10.1093","volume":"24","author":[{"given":"Lun","family":"Li","sequence":"first","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Xu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongmei","family":"Tian","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anke","family":"Wang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junwei","family":"Zhu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cuiping","family":"Li","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Na","family":"Li","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhao","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leisheng","family":"Shi","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation , Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongbiao","family":"Xue","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhang","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiming","family":"Bao","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenming","family":"Zhao","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuhui","family":"Song","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,12]]},"reference":[{"key":"2023052022430731000_ref1","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1093\/genetics\/141.2.743","article-title":"Mitochondrial portraits of human populations using median networks","volume":"141","author":"Bandelt","year":"1995","journal-title":"Genetics"},{"key":"2023052022430731000_ref2","first-page":"591","article-title":"Combined analyses of chloroplast DNA haplotypes and microsatellite markers reveal new insights into the origin and dissemination route of cultivated pears native to East Asia, Frontiers","volume":"9","author":"Yue","year":"2018","journal-title":"Plant Sci"},{"key":"2023052022430731000_ref3","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/oxfordjournals.molbev.a026036","article-title":"Median-joining networks for inferring intraspecific phylogenies","volume":"16","author":"Bandelt","year":"1999","journal-title":"Mol Biol Evol"},{"key":"2023052022430731000_ref4","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1093\/genetics\/132.2.619","article-title":"A cladistic-analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA-sequence data.3. Cladogram estimation","volume":"132","author":"Templeton","year":"1992","journal-title":"Genetics"},{"key":"2023052022430731000_ref5","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1111\/2041-210X.12969","article-title":"Analysis of haplotype networks: the randomized minimum spanning tree method","volume":"9","author":"Paradis","year":"2018","journal-title":"Methods in Ecology and Evolution"},{"key":"2023052022430731000_ref6","doi-asserted-by":"crossref","first-page":"423","DOI":"10.3389\/fgene.2019.00423","article-title":"A first Y-chromosomal haplotype network to investigate male-driven population dynamics in domestic and wild Bactrian camels","volume":"10","author":"Felkel","year":"2019","journal-title":"Front Genet"},{"key":"2023052022430731000_ref7","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.gpb.2020.09.001","article-title":"The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR","volume":"18","author":"Song","year":"2020","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2023052022430731000_ref8","first-page":"212","article-title":"The 2019 novel coronavirus resource","volume":"42","author":"Zhao","year":"2020","journal-title":"Yi Chuan"},{"key":"2023052022430731000_ref9","doi-asserted-by":"crossref","first-page":"20198","DOI":"10.1073\/pnas.2006824117","article-title":"Haplotype networks of SARS-CoV-2 infections in the diamond princess cruise ship outbreak","volume":"117","author":"Sekizuka","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023052022430731000_ref10","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1007\/s11357-020-00195-z","article-title":"Nursing homes and the elderly regarding the COVID-19 pandemic: situation report from Hungary","volume":"42","author":"Kemenesi","year":"2020","journal-title":"GeroScience"},{"key":"2023052022430731000_ref11","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.gpb.2021.08.007","article-title":"Genomic epidemiology of SARS-CoV-2 in Pakistan","volume":"19","author":"Song","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2023052022430731000_ref12","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"InterJournal, Complex Systems"},{"key":"2023052022430731000_ref13","first-page":"361","article-title":"Gephi: an open source software for exploring and manipulating networks, proceedings of the international AAAI conference on web and social","volume":"3","author":"Bastian","year":"2009","journal-title":"Media"},{"key":"2023052022430731000_ref14","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s40294-016-0017-8","article-title":"Analysis and visualization of large networks with program package Pajek","volume":"4","author":"Mrvar","year":"2016","journal-title":"Complex Adaptive Systems Modeling"},{"key":"2023052022430731000_ref15","first-page":"1","volume-title":"Encyclopedia of Social Network Analysis and Mining","author":"Auber","year":"2017"},{"key":"2023052022430731000_ref16","first-page":"119","volume-title":"WiGis: A Framework for Scalable Web-Based Interactive Graph Visualizations","author":"Gretarsson","year":"2009"},{"key":"2023052022430731000_ref17","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2023052022430731000_ref18","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/1471-2105-5-17","article-title":"VisANT: an online visualization and analysis tool for biological interaction data","volume":"5","author":"Hu","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023052022430731000_ref19","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"Popart: full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods in Ecology and Evolution"},{"key":"2023052022430731000_ref20","doi-asserted-by":"crossref","article-title":"CoV genome tracker: tracing genomic footprints of Covid-19 pandemic","author":"Akther","DOI":"10.1101\/2020.04.10.036343"},{"key":"2023052022430731000_ref21","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac399","article-title":"TPD: a web tool for tipping-point detection based on dynamic network biomarker","volume":"23","author":"Chen","year":"2022","journal-title":"Brief Bioinform"},{"key":"2023052022430731000_ref22","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1090\/S0002-9939-1989-0967486-0","article-title":"A greedoid polynomial which distinguishes rooted arborescences","volume":"107","author":"Gordon","year":"1989","journal-title":"Proceedings of the American Mathematical Society"},{"key":"2023052022430731000_ref23","first-page":"112","article-title":"The minimum evolution problem: overview and classification, networks: an","volume":"53","author":"Catanzaro","year":"2009","journal-title":"International Journal"},{"key":"2023052022430731000_ref24","doi-asserted-by":"crossref","first-page":"233","DOI":"10.6028\/jres.071B.032","article-title":"Optimum branchings","volume":"71","author":"Edmonds","year":"1967","journal-title":"Journal of Research of the national Bureau of Standards B"},{"key":"2023052022430731000_ref25","first-page":"1396","article-title":"On the shortest arborescence of a directed graph","volume":"14","author":"Chu","year":"1965","journal-title":"Sci Sin"},{"key":"2023052022430731000_ref26","first-page":"0184","volume-title":"Parallel and Distributed Processing Symposium, International","author":"Clement","year":"2002"},{"key":"2023052022430731000_ref27","doi-asserted-by":"crossref","first-page":"2297","DOI":"10.1016\/j.scib.2021.02.012","article-title":"Evolutionary analysis and lineage designation of SARS-CoV-2 genomes","volume":"66","author":"Tang","year":"2021","journal-title":"Science Bulletin"},{"key":"2023052022430731000_ref28","doi-asserted-by":"crossref","DOI":"10.1126\/science.add4153","article-title":"Multiple lineages of Monkeypox virus detected in the United States, 2021-2022","author":"Gigante","year":"2022"},{"key":"2023052022430731000_ref29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-022-29614-9","article-title":"Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic","volume":"13","author":"Patrono","year":"2022","journal-title":"Nat Commun"},{"key":"2023052022430731000_ref30","doi-asserted-by":"crossref","DOI":"10.1103\/PhysRevE.70.066111","article-title":"Finding community structure in very large networks","volume":"70","author":"Clauset","year":"2004","journal-title":"Physical Review E"},{"key":"2023052022430731000_ref31","doi-asserted-by":"crossref","first-page":"2422","DOI":"10.1016\/j.cell.2022.06.005","article-title":"Antibody escape of SARS-CoV-2 omicron BA.4 and BA.5 from vaccine and BA.1 serum","volume":"185","author":"Tuekprakhon","year":"2022","journal-title":"Cell"},{"key":"2023052022430731000_ref32","doi-asserted-by":"crossref","first-page":"1442","DOI":"10.3201\/eid2807.220526","article-title":"SARS-CoV-2 Delta-omicron recombinant viruses, United States","volume":"28","author":"Lacek","year":"2022","journal-title":"Emerg Infect Dis"},{"key":"2023052022430731000_ref33","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1038\/s41586-022-05189-9","article-title":"Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape","volume":"609","author":"Turakhia","year":"2022","journal-title":"Nature"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/3\/bbad174\/50410948\/bbad174.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/3\/bbad174\/50410948\/bbad174.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T22:45:02Z","timestamp":1684622702000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad174\/7159163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5]]},"references-count":33,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,5,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad174","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,5]]},"published":{"date-parts":[[2023,5]]},"article-number":"bbad174"}}