{"id":"https://openalex.org/W2951757951","doi":"https://doi.org/10.1093/bioinformatics/btx155","title":"IcyTree: rapid browser-based visualization for phylogenetic trees and networks","display_name":"IcyTree: rapid browser-based visualization for phylogenetic trees and networks","publication_year":2017,"publication_date":"2017-03-22","ids":{"openalex":"https://openalex.org/W2951757951","doi":"https://doi.org/10.1093/bioinformatics/btx155","mag":"2951757951","pmid":"https://pubmed.ncbi.nlm.nih.gov/28407035"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx155","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/15/2392/25157664/btx155.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/33/15/2392/25157664/btx155.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088841943","display_name":"Timothy G. Vaughan","orcid":null},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Timothy G Vaughan","raw_affiliation_strings":["Department of Computer Science, University of Auckland, Auckland, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5088841943"],"corresponding_institution_ids":["https://openalex.org/I154130895"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":4.0698,"has_fulltext":true,"cited_by_count":134,"citation_normalized_percentile":{"value":0.95173184,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"15","first_page":"2392","last_page":"2394"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5257999897003174,"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":0.5257999897003174,"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/T10895","display_name":"Species Distribution and Climate Change","score":0.1388999968767166,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12359","display_name":"Fern and Epiphyte Biology","score":0.052000001072883606,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7899587154388428},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7070764899253845},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5766695737838745},{"id":"https://openalex.org/keywords/phylogenetic-relationship","display_name":"Phylogenetic relationship","score":0.4131094813346863},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35658055543899536},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.24128508567810059},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11416542530059814},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.057399362325668335}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7899587154388428},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7070764899253845},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5766695737838745},{"id":"https://openalex.org/C2992072516","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetic relationship","level":4,"score":0.4131094813346863},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35658055543899536},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.24128508567810059},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11416542530059814},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.057399362325668335}],"mesh":[{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","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":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx155","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/15/2392/25157664/btx155.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":"pmh:oai:pubmedcentral.nih.gov:5860111","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860111","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:28407035","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28407035","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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx155","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/15/2392/25157664/btx155.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":[],"awards":[{"id":"https://openalex.org/G4951381499","display_name":null,"funder_award_id":"UOA1324","funder_id":"https://openalex.org/F4320320774","funder_display_name":"Royal Society Te Ap\u0101rangi"}],"funders":[{"id":"https://openalex.org/F4320320774","display_name":"Royal Society Te Ap\u0101rangi","ror":"https://ror.org/04tajb587"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951757951.pdf","grobid_xml":"https://content.openalex.org/works/W2951757951.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1981275193","https://openalex.org/W2026062398","https://openalex.org/W2097734528","https://openalex.org/W2100412820","https://openalex.org/W2103546861","https://openalex.org/W2132247062","https://openalex.org/W2139871526","https://openalex.org/W2148698435","https://openalex.org/W2162371815","https://openalex.org/W2170041483","https://openalex.org/W2566768616","https://openalex.org/W3199943451","https://openalex.org/W4233815609","https://openalex.org/W6800717233"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W3150750732","https://openalex.org/W2388579761","https://openalex.org/W2386173511","https://openalex.org/W4254698667","https://openalex.org/W903818084","https://openalex.org/W2982036139","https://openalex.org/W2352802959","https://openalex.org/W3202916294","https://openalex.org/W2375151634"],"abstract_inverted_index":{"SUMMARY:":[0],"IcyTree":[1,27,63,86,109,129],"is":[2,87,110,130,137],"an":[3],"easy-to-use":[4],"application":[5,90],"which":[6],"can":[7,92],"be":[8,93],"used":[9],"to":[10,127],"visualize":[11],"a":[12,32,37,88],"wide":[13],"variety":[14],"of":[15,77,80,145],"phylogenetic":[16,22,42,75],"trees":[17,52,76],"and":[18,49,68,91,106,133],"networks.":[19],"While":[20],"numerous":[21],"tree":[23],"viewers":[24],"exist":[25],"already,":[26],"distinguishes":[28],"itself":[29],"by":[30],"being":[31],"purely":[33],"online":[34],"tool,":[35],"having":[36],"responsive":[38],"user":[39],"interface,":[40],"supporting":[41],"networks":[43],"(ancestral":[44],"recombination":[45],"graphs":[46],"in":[47,113],"particular),":[48],"efficiently":[50],"drawing":[51],"that":[53,71],"include":[54,103],"information":[55],"such":[56],"as":[57],"ancestral":[58],"locations":[59],"or":[60],"trait":[61],"values.":[62],"also":[64],"provides":[65],"intuitive":[66],"panning":[67],"zooming":[69],"utilities":[70],"make":[72],"exploring":[73],"large":[74],"many":[78],"thousands":[79],"taxa":[81],"feasible.":[82],"AVAILABILITY":[83],"AND":[84],"IMPLEMENTATION:":[85],"web":[89,101],"accessed":[94],"directly":[95],"at":[96,140],"http://tgvaughan.github.com/icytree":[97],".":[98],"Currently":[99],"supported":[100],"browsers":[102],"Mozilla":[104],"Firefox":[105],"Google":[107],"Chrome.":[108],"written":[111],"entirely":[112],"client-side":[114],"JavaScript":[115],"(no":[116],"plugin":[117],"required)":[118],"and,":[119],"once":[120],"loaded,":[121],"does":[122],"not":[123],"require":[124],"network":[125],"access":[126],"run.":[128],"free":[131],"software,":[132],"the":[134,146],"source":[135],"code":[136],"made":[138],"available":[139],"http://github.com/tgvaughan/icytree":[141],"under":[142],"version":[143],"3":[144],"GNU":[147],"General":[148],"Public":[149],"License.":[150],"CONTACT:":[151],"tgvaughan@gmail.com.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":21},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
