{"id":"https://openalex.org/W4366234886","doi":"https://doi.org/10.1093/nar/gkad284","title":"Haplogrep 3 -\u00a0an\u00a0interactive haplogroup classification and analysis platform","display_name":"Haplogrep 3 -\u00a0an\u00a0interactive haplogroup classification and analysis platform","publication_year":2023,"publication_date":"2023-04-18","ids":{"openalex":"https://openalex.org/W4366234886","doi":"https://doi.org/10.1093/nar/gkad284","pmid":"https://pubmed.ncbi.nlm.nih.gov/37070190"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkad284","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad284","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad284/50004767/gkad284.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad284/50004767/gkad284.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109584850","display_name":"Sebastian Sch\u00f6nherr","orcid":null},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Sebastian Sch\u00f6nherr","raw_affiliation_strings":["Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria"],"affiliations":[{"raw_affiliation_string":"Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055515363","display_name":"Hansi Wei\u00dfensteiner","orcid":"https://orcid.org/0000-0002-2871-8669"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Hansi Weissensteiner","raw_affiliation_strings":["Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria"],"affiliations":[{"raw_affiliation_string":"Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082464365","display_name":"Florian Kronenberg","orcid":"https://orcid.org/0000-0003-2229-1120"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Florian Kronenberg","raw_affiliation_strings":["Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria"],"affiliations":[{"raw_affiliation_string":"Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029740420","display_name":"Lukas Forer","orcid":"https://orcid.org/0000-0003-2139-7329"},"institutions":[{"id":"https://openalex.org/I143397708","display_name":"Innsbruck Medical University","ror":"https://ror.org/03pt86f80","country_code":"AT","type":"education","lineage":["https://openalex.org/I143397708"]},{"id":"https://openalex.org/I190249584","display_name":"Universit\u00e4t Innsbruck","ror":"https://ror.org/054pv6659","country_code":"AT","type":"education","lineage":["https://openalex.org/I190249584"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Lukas Forer","raw_affiliation_strings":["Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria"],"affiliations":[{"raw_affiliation_string":"Institute of Genetic Epidemiology, Medical University of Innsbruck , Innsbruck \u00a06020, Austria","institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5029740420"],"corresponding_institution_ids":["https://openalex.org/I143397708","https://openalex.org/I190249584"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":19.1161,"has_fulltext":true,"cited_by_count":126,"citation_normalized_percentile":{"value":0.9960968,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"51","issue":"W1","first_page":"W263","last_page":"W268"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6597449779510498},{"id":"https://openalex.org/keywords/haplogroup","display_name":"Haplogroup","score":0.5712448358535767},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5432165861129761},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.500471830368042},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4624287188053131},{"id":"https://openalex.org/keywords/biobank","display_name":"Biobank","score":0.4595964848995209},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4440818428993225},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43519556522369385},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33445465564727783},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33053895831108093},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32938623428344727},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2829517126083374},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2580677270889282},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.08389678597450256}],"concepts":[{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6597449779510498},{"id":"https://openalex.org/C201526758","wikidata":"https://www.wikidata.org/wiki/Q80686","display_name":"Haplogroup","level":5,"score":0.5712448358535767},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5432165861129761},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.500471830368042},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4624287188053131},{"id":"https://openalex.org/C116567970","wikidata":"https://www.wikidata.org/wiki/Q864217","display_name":"Biobank","level":2,"score":0.4595964848995209},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4440818428993225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43519556522369385},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33445465564727783},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33053895831108093},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32938623428344727},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2829517126083374},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2580677270889282},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.08389678597450256},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004272","descriptor_name":"DNA, Mitochondrial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004272","descriptor_name":"DNA, Mitochondrial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004272","descriptor_name":"DNA, Mitochondrial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008928","descriptor_name":"Mitochondria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008928","descriptor_name":"Mitochondria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008928","descriptor_name":"Mitochondria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkad284","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad284","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad284/50004767/gkad284.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:37070190","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37070190","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10320078","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10320078","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10320078/pdf/gkad284.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkad284","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkad284","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad284/50004767/gkad284.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320326164","display_name":"Medizinische Universit\u00e4t Innsbruck","ror":"https://ror.org/03pt86f80"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4366234886.pdf"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1520910338","https://openalex.org/W1546375972","https://openalex.org/W2005581687","https://openalex.org/W2037764582","https://openalex.org/W2051309999","https://openalex.org/W2104549677","https://openalex.org/W2111668248","https://openalex.org/W2336818861","https://openalex.org/W2617478587","https://openalex.org/W3037947787","https://openalex.org/W3044375621","https://openalex.org/W3069520935","https://openalex.org/W3162304089","https://openalex.org/W3165158097","https://openalex.org/W3165188253","https://openalex.org/W3205807109","https://openalex.org/W4221033829","https://openalex.org/W4221070908","https://openalex.org/W4280540551","https://openalex.org/W4294012180","https://openalex.org/W4297093198","https://openalex.org/W4379745724","https://openalex.org/W4394666350","https://openalex.org/W6674561012","https://openalex.org/W6780918678"],"related_works":["https://openalex.org/W4285087457","https://openalex.org/W3113746618","https://openalex.org/W4226051228","https://openalex.org/W3017691140","https://openalex.org/W4384208482","https://openalex.org/W4244742767","https://openalex.org/W2470939431","https://openalex.org/W2024651825","https://openalex.org/W4401623684","https://openalex.org/W4395677717"],"abstract_inverted_index":{"Over":[0],"the":[1,14,49,71,132,147,151],"last":[2],"decade,":[3],"Haplogrep":[4,30],"has":[5,53],"become":[6],"a":[7,67,97,119],"standard":[8],"tool":[9],"for":[10,33,124],"haplogroup":[11,76],"classification":[12,112],"in":[13,150],"field":[15],"of":[16,35,137],"human":[17],"mitochondrial":[18],"DNA":[19],"and":[20,27,41,79,117,156],"is":[21],"widely":[22],"used":[23],"by":[24,73],"medical,":[25],"forensic,":[26],"evolutionary":[28],"researchers.":[29],"scales":[31],"well":[32],"thousands":[34,136],"samples,":[36],"supports":[37],"many":[38],"file":[39],"formats":[40],"provides":[42],"an":[43,89],"intuitive":[44],"graphical":[45],"web":[46,100,154],"interface.":[47],"Nevertheless,":[48],"currently":[50],"available":[51,85],"version":[52],"limitations":[54],"when":[55],"applying":[56],"it":[57],"to":[58,70,91,109,134,145],"large":[59,103],"biobank-scale":[60],"data.":[61],"In":[62],"this":[63],"paper,":[64],"we":[65],"present":[66],"major":[68],"upgrade":[69],"software":[72],"adding":[74],"(a)":[75],"summary":[77],"statistics":[78],"variant":[80],"annotations":[81],"from":[82],"various":[83],"publicly":[84],"genome":[86],"databases,":[87],"(b)":[88],"interface":[90],"connect":[92],"new":[93,98],"phylogenetic":[94],"trees,":[95],"(c)":[96],"state-of-the-art":[99],"framework":[101],"managing":[102],"scale":[104],"data,":[105],"(d)":[106],"algorithmic":[107],"adaptions":[108],"improve":[110],"FASTA":[111],"using":[113],"BWA-specific":[114],"alignment":[115],"rules":[116],"(e)":[118],"pre-classification":[120],"quality":[121],"control":[122],"step":[123],"VCF":[125],"samples.":[126],"These":[127],"improvements":[128],"will":[129],"give":[130],"researchers":[131],"opportunity":[133],"classify":[135],"samples":[138],"as":[139],"usual":[140],"but":[141],"providing":[142],"additional":[143],"ways":[144],"investigate":[146],"dataset":[148],"directly":[149],"browser.":[152],"The":[153],"service":[155],"its":[157],"documentation":[158],"can":[159],"be":[160],"accessed":[161],"freely":[162],"without":[163],"any":[164],"registration":[165],"at":[166],"https://haplogrep.i-med.ac.at.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":24},{"year":2025,"cited_by_count":64},{"year":2024,"cited_by_count":29},{"year":2023,"cited_by_count":9}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
