{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T03:44:42Z","timestamp":1775706282197,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,8,17]],"date-time":"2020-08-17T00:00:00Z","timestamp":1597622400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"EUROTAST Marie Curie Framework Programme 7 Initial Training Network","award":["290344"],"award-info":[{"award-number":["290344"]}]},{"name":"The Research Fund of University of Iceland for doctoral studies"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species\u2014given an extant annotated phylogenetic tree defined by sequence variants.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The software is available at the following URL https:\/\/gitlab.com\/bio_anth_decode\/haploGrouper.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa729","type":"journal-article","created":{"date-parts":[[2020,8,12]],"date-time":"2020-08-12T19:32:50Z","timestamp":1597260770000},"page":"570-572","source":"Crossref","is-referenced-by-count":42,"title":["HaploGrouper: a generalized approach to haplogroup classification"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7579-9713","authenticated-orcid":false,"given":"Anuradha","family":"Jagadeesan","sequence":"first","affiliation":[{"name":"deCODE Genetics\/Amgen , Reykjavik 101, Iceland"},{"name":"Department of Anthropology, University of Iceland , Reykjavik 101, Iceland"}]},{"given":"S Sunna","family":"Ebenesersd\u00f3ttir","sequence":"additional","affiliation":[{"name":"deCODE Genetics\/Amgen , Reykjavik 101, Iceland"},{"name":"Department of Anthropology, University of Iceland , Reykjavik 101, Iceland"}]},{"given":"Valdis B","family":"Gu\u00f0mundsd\u00f3ttir","sequence":"additional","affiliation":[{"name":"deCODE Genetics\/Amgen , Reykjavik 101, Iceland"},{"name":"Department of Anthropology, University of Iceland , Reykjavik 101, Iceland"}]},{"given":"Elisabet Linda","family":"Thordardottir","sequence":"additional","affiliation":[{"name":"deCODE Genetics\/Amgen , Reykjavik 101, Iceland"}]},{"given":"Kristjan H S","family":"Moore","sequence":"additional","affiliation":[{"name":"deCODE Genetics\/Amgen , Reykjavik 101, Iceland"}]},{"given":"Agnar","family":"Helgason","sequence":"additional","affiliation":[{"name":"deCODE Genetics\/Amgen , Reykjavik 101, Iceland"},{"name":"Department of Anthropology, University of Iceland , Reykjavik 101, Iceland"}]}],"member":"286","published-online":{"date-parts":[[2020,8,17]]},"reference":[{"key":"2023051706072911300_btaa729-B1","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/j.mito.2010.09.013","article-title":"MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations","volume":"11","author":"Fan","year":"2011","journal-title":"Mitochondrion"},{"key":"2023051706072911300_btaa729-B2","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1093\/bioinformatics\/btu825","article-title":"Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier","volume":"31","author":"Navarro-Gomez","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051706072911300_btaa729-B3","author":"Poznik","year":"2016"},{"key":"2023051706072911300_btaa729-B4","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/j.fsigen.2013.07.005","article-title":"Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA)","volume":"7","author":"R\u00f6ck","year":"2013","journal-title":"Forensic Sci. 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