{"id":"https://openalex.org/W2149057166","doi":"https://doi.org/10.1093/bioinformatics/17.4.383","title":"ATV: display and manipulation of annotated phylogenetic trees","display_name":"ATV: display and manipulation of annotated phylogenetic trees","publication_year":2001,"publication_date":"2001-04-01","ids":{"openalex":"https://openalex.org/W2149057166","doi":"https://doi.org/10.1093/bioinformatics/17.4.383","mag":"2149057166","pmid":"https://pubmed.ncbi.nlm.nih.gov/11301314"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/17.4.383","doi":"https://doi.org/10.1093/bioinformatics/17.4.383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/17.4.383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/17/4/383/48837068/bioinformatics_17_4_383.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W2149057166"],"child_works_count":0,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/17/4/383/48837068/bioinformatics_17_4_383.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079950186","display_name":"Christian M. Zmasek","orcid":"https://orcid.org/0000-0002-7933-2424","observed_orcids":["https://orcid.org/0000-0002-7933-2424"]},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christian M. Zmasek","raw_affiliation_strings":["Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020118397","display_name":"Sean R. Eddy","orcid":"https://orcid.org/0000-0001-6676-4706","observed_orcids":["https://orcid.org/0000-0001-6676-4706"]},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean R. Eddy","raw_affiliation_strings":["Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":3.7507,"has_fulltext":true,"cited_by_count":279,"citation_normalized_percentile":{"value":0.94688359,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"17","issue":"4","first_page":"383","last_page":"384"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9984999895095825,"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":0.9984999895095825,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.0003000000142492354,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"phylogenetic tree","score":0.7730000019073486},{"id":"https://openalex.org/keywords/tree-visualization","display_name":"tree visualization","score":0.8489999771118164},{"id":"https://openalex.org/keywords/tree-manipulation","display_name":"tree manipulation","score":0.8889999985694885},{"id":"https://openalex.org/keywords/java-programs","display_name":"Java programs","score":0.6830000281333923},{"id":"https://openalex.org/keywords/foresters","display_name":"foresters","score":0.5199999809265137}],"concepts":[{"id":"https://openalex.org/C169485995","wikidata":"https://www.wikidata.org/wiki/Q42283","display_name":"File Transfer Protocol","level":3,"score":0.5499229431152344},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4725073575973511},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4252975285053253},{"id":"https://openalex.org/C2781092335","wikidata":"https://www.wikidata.org/wiki/Q867132","display_name":"Diva","level":2,"score":0.4215776324272156},{"id":"https://openalex.org/C15524039","wikidata":"https://www.wikidata.org/wiki/Q865817","display_name":"Java applet","level":3,"score":0.41677093505859375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40809935331344604},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.36643674969673157},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3433198034763336},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.24137309193611145},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20813333988189697},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.16835656762123108},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13584327697753906},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/17.4.383","doi":"https://doi.org/10.1093/bioinformatics/17.4.383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/17.4.383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/17/4/383/48837068/bioinformatics_17_4_383.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:11301314","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11301314","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,"listed_in":[],"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"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.28.9540","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.28.9540","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.genetics.wustl.edu/pub/eddy/papers/2001-zmasek-atv/preprint.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/17.4.383","doi":"https://doi.org/10.1093/bioinformatics/17.4.383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/17.4.383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/17/4/383/48837068/bioinformatics_17_4_383.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149057166.pdf","grobid_xml":"https://content.openalex.org/works/W2149057166.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2055043387","https://openalex.org/W2057081312","https://openalex.org/W2098811647","https://openalex.org/W2141885858","https://openalex.org/W2150297520","https://openalex.org/W3199943451","https://openalex.org/W7099253376"],"related_works":["https://openalex.org/W7098156622","https://openalex.org/W4372333115","https://openalex.org/W2151602856","https://openalex.org/W2170166964","https://openalex.org/W7097891131","https://openalex.org/W2142008033","https://openalex.org/W2117118889","https://openalex.org/W2099836453","https://openalex.org/W2111554887"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"A":[2],"Tree":[3],"Viewer":[4],"(ATV)":[5],"is":[6,38],"a":[7,25,33],"Java":[8],"tool":[9],"for":[10],"the":[11],"display":[12],"and":[13,28,44],"manipulation":[14],"of":[15],"annotated":[16],"phylogenetic":[17],"trees.":[18],"It":[19],"can":[20],"be":[21],"utilized":[22],"both":[23],"as":[24,29],"standalone":[26],"application":[27],"an":[30],"applet":[31],"in":[32],"web":[34],"browser.":[35],"Availability:":[36],"ATV":[37],"available":[39],"via":[40,45],"WWW":[41],"at":[42,47],"http://www.genetics.wustl.edu/eddy/atv/":[43],"FTP":[46],"ftp://ftp.genetics.wustl.edu/pub/eddy/software/forester.tar.Z":[48],"Contact:":[49],"eddy@genetics.wustl.edu":[50]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":13}],"updated_date":"2026-11-14T11:04:58.165337","created_date":"2016-06-24T00:00:00"}
