{"id":"https://openalex.org/W2949182334","doi":"https://doi.org/10.1093/bioinformatics/btx610","title":"Phandango: an interactive viewer for bacterial population genomics","display_name":"Phandango: an interactive viewer for bacterial population genomics","publication_year":2017,"publication_date":"2017-09-23","ids":{"openalex":"https://openalex.org/W2949182334","doi":"https://doi.org/10.1093/bioinformatics/btx610","mag":"2949182334","pmid":"https://pubmed.ncbi.nlm.nih.gov/29028899"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx610","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx610","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/2/292/25114265/btx610.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/2/292/25114265/btx610.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001836904","display_name":"James Hadfield","orcid":"https://orcid.org/0000-0002-4118-6468"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"James Hadfield","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029973916","display_name":"Nicholas J. Croucher","orcid":"https://orcid.org/0000-0001-6303-8768"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicholas J Croucher","raw_affiliation_strings":["Department of Infectious Disease Epidemiology, Imperial College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Disease Epidemiology, Imperial College London, London, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029877713","display_name":"Richard Goater","orcid":"https://orcid.org/0000-0001-9954-841X"},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard J Goater","raw_affiliation_strings":["Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK","institution_ids":["https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028032976","display_name":"Khalil Abudahab","orcid":null},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Khalil Abudahab","raw_affiliation_strings":["Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK","institution_ids":["https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068117269","display_name":"David M. Aanensen","orcid":"https://orcid.org/0000-0001-6688-0854"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David M Aanensen","raw_affiliation_strings":["Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK","Department of Infectious Disease Epidemiology, Imperial College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Genomic Pathogen Surveillance, Wellcome Trust Genome Campus, Cambridge, UK","institution_ids":["https://openalex.org/I87048295"]},{"raw_affiliation_string":"Department of Infectious Disease Epidemiology, Imperial College London, London, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049639550","display_name":"Simon R. Harris","orcid":"https://orcid.org/0000-0003-1512-6194"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Simon R Harris","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001836904"],"corresponding_institution_ids":["https://openalex.org/I2802476451"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":20.4151,"has_fulltext":false,"cited_by_count":660,"citation_normalized_percentile":{"value":0.99659394,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"34","issue":"2","first_page":"292","last_page":"293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2930000126361847,"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":0.2930000126361847,"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/T12492","display_name":"Zoonotic diseases and public health","score":0.05139999836683273,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.039900001138448715,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.737993061542511},{"id":"https://openalex.org/keywords/population-genomics","display_name":"Population genomics","score":0.6608861684799194},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6416898965835571},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5634806752204895},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5535627603530884},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4552137553691864},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.41483309864997864},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3441011309623718},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.17758190631866455},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1525058150291443},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0639835000038147},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06084105372428894}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.737993061542511},{"id":"https://openalex.org/C2779040068","wikidata":"https://www.wikidata.org/wiki/Q7229807","display_name":"Population genomics","level":5,"score":0.6608861684799194},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6416898965835571},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5634806752204895},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5535627603530884},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4552137553691864},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.41483309864997864},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3441011309623718},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.17758190631866455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1525058150291443},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0639835000038147},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06084105372428894},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","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}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx610","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx610","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/2/292/25114265/btx610.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29028899","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29028899","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5860215","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860215","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/55836","is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/55836","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"293","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx610","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx610","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/2/292/25114265/btx610.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.6800000071525574,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G6299046169","display_name":null,"funder_award_id":"099202","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G7274432344","display_name":null,"funder_award_id":"098051","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2949182334.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1972145956","https://openalex.org/W2037409969","https://openalex.org/W2080618984","https://openalex.org/W2122673596","https://openalex.org/W2148687236","https://openalex.org/W2161633633","https://openalex.org/W2560057613","https://openalex.org/W2949477823"],"related_works":["https://openalex.org/W1595358351","https://openalex.org/W2939866924","https://openalex.org/W4233657210","https://openalex.org/W3113639865","https://openalex.org/W4387060328","https://openalex.org/W2435275176","https://openalex.org/W2102597440","https://openalex.org/W2528393243","https://openalex.org/W1559459518","https://openalex.org/W4240632926"],"abstract_inverted_index":{"SUMMARY:":[0],"Fully":[1],"exploiting":[2],"the":[3,73],"wealth":[4],"of":[5,19,23,30,38,67,105],"data":[6],"in":[7,26,60,80],"current":[8],"bacterial":[9],"population":[10,69],"genomics":[11,70],"datasets":[12,71,106],"requires":[13],"synthesizing":[14],"and":[15,42,83,100],"integrating":[16],"different":[17],"types":[18],"analysis":[20,44,78],"across":[21],"millions":[22],"base":[24],"pairs":[25],"hundreds":[27],"or":[28],"thousands":[29],"isolates.":[31],"Current":[32],"approaches":[33],"often":[34],"use":[35,97],"static":[36],"representations":[37],"phylogenetic,":[39],"epidemiological,":[40],"statistical":[41],"evolutionary":[43],"results":[45],"that":[46],"are":[47],"difficult":[48],"to":[49,51],"relate":[50],"one":[52],"another.":[53],"Phandango":[54,89],"is":[55,90,117],"an":[56,81],"interactive":[57,84],"application":[58,93],"running":[59],"a":[61,91,102,113],"web":[62,92],"browser":[63],"allowing":[64],"fast":[65],"exploration":[66],"large-scale":[68],"combining":[72],"output":[74],"from":[75],"multiple":[76],"genomic":[77],"methods":[79],"intuitive":[82],"manner.":[85],"AVAILABILITY":[86],"AND":[87],"IMPLEMENTATION:":[88],"freely":[94],"available":[95,118],"for":[96],"at":[98,121],"www.phandango.net":[99],"includes":[101],"diverse":[103],"collection":[104],"as":[107],"examples.":[108],"Source":[109],"code":[110],"together":[111],"with":[112],"detailed":[114],"wiki":[115],"page":[116],"on":[119],"GitHub":[120],"https://github.com/jameshadfield/phandango.":[122]},"counts_by_year":[{"year":2026,"cited_by_count":30},{"year":2025,"cited_by_count":59},{"year":2024,"cited_by_count":92},{"year":2023,"cited_by_count":108},{"year":2022,"cited_by_count":80},{"year":2021,"cited_by_count":109},{"year":2020,"cited_by_count":74},{"year":2019,"cited_by_count":57},{"year":2018,"cited_by_count":42},{"year":2017,"cited_by_count":9}],"updated_date":"2026-06-18T10:00:31.954636","created_date":"2025-10-10T00:00:00"}
