{"id":"https://openalex.org/W2111554887","doi":"https://doi.org/10.1186/1751-0473-2-7","title":"TreeViewJ: An application for viewing and analyzing phylogenetic trees","display_name":"TreeViewJ: An application for viewing and analyzing phylogenetic trees","publication_year":2007,"publication_date":"2007-10-31","ids":{"openalex":"https://openalex.org/W2111554887","doi":"https://doi.org/10.1186/1751-0473-2-7","mag":"2111554887","pmid":"https://pubmed.ncbi.nlm.nih.gov/17974028"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-2-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-7","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-7","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086629705","display_name":"Matthew Peterson","orcid":"https://orcid.org/0000-0003-4422-4463"},"institutions":[{"id":"https://openalex.org/I44896327","display_name":"Mitre (United States)","ror":"https://ror.org/03ks2a131","country_code":"US","type":"company","lineage":["https://openalex.org/I44896327"]},{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew W Peterson","raw_affiliation_strings":["Department of Biomedical Engineering, Boston University, 44 Cummington St, Boston, MA, USA","The MITRE Corporation, 202 Burlington Rd, Bedford, MA, USA","Department of Biomedical Engineering, Boston University, Boston, USA","The MITRE Corporation, Bedford, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, 44 Cummington St, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"The MITRE Corporation, 202 Burlington Rd, Bedford, MA, USA","institution_ids":["https://openalex.org/I44896327"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, USA","institution_ids":[]},{"raw_affiliation_string":"The MITRE Corporation, Bedford, USA","institution_ids":["https://openalex.org/I44896327"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082822281","display_name":"Marc Colosimo","orcid":null},"institutions":[{"id":"https://openalex.org/I44896327","display_name":"Mitre (United States)","ror":"https://ror.org/03ks2a131","country_code":"US","type":"company","lineage":["https://openalex.org/I44896327"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marc E Colosimo","raw_affiliation_strings":["The MITRE Corporation, 202 Burlington Rd, Bedford, MA, USA","The MITRE Corporation Bedford, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The MITRE Corporation, 202 Burlington Rd, Bedford, MA, USA","institution_ids":["https://openalex.org/I44896327"]},{"raw_affiliation_string":"The MITRE Corporation Bedford, USA","institution_ids":["https://openalex.org/I44896327"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5086629705"],"corresponding_institution_ids":["https://openalex.org/I111088046","https://openalex.org/I44896327"],"apc_list":null,"apc_paid":null,"fwci":0.2691,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.59614021,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"2","issue":"1","first_page":"7","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5565999746322632,"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":0.5565999746322632,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.08940000087022781,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10895","display_name":"Species Distribution and Climate Change","score":0.05979999899864197,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8092728853225708},{"id":"https://openalex.org/keywords/timeline","display_name":"Timeline","score":0.7976150512695312},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7144807577133179},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6266528964042664},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5738019943237305},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5590806007385254},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5331271290779114},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5286427140235901},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.48981592059135437},{"id":"https://openalex.org/keywords/sort","display_name":"sort","score":0.463522732257843},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4459729790687561},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4001723527908325},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.37205079197883606},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3322879672050476},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24068084359169006},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16416925191879272},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.12438198924064636},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11069780588150024},{"id":"https://openalex.org/keywords/archaeology","display_name":"Archaeology","score":0.08076062798500061}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8092728853225708},{"id":"https://openalex.org/C4438859","wikidata":"https://www.wikidata.org/wiki/Q186117","display_name":"Timeline","level":2,"score":0.7976150512695312},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7144807577133179},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6266528964042664},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5738019943237305},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5590806007385254},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5331271290779114},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5286427140235901},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.48981592059135437},{"id":"https://openalex.org/C88548561","wikidata":"https://www.wikidata.org/wiki/Q347599","display_name":"sort","level":2,"score":0.463522732257843},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4459729790687561},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4001723527908325},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.37205079197883606},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3322879672050476},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24068084359169006},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16416925191879272},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.12438198924064636},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11069780588150024},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.08076062798500061},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":5,"locations":[{"id":"doi:10.1186/1751-0473-2-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-7","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-7","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:17974028","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17974028","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:doaj.org/article:cdf5e6caaa634c44a3f84f41bf8bbaa9","is_oa":false,"landing_page_url":"https://doaj.org/article/cdf5e6caaa634c44a3f84f41bf8bbaa9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code for Biology and Medicine, Vol 2, Iss 1, p 7 (2007)","raw_type":"article"},{"id":"pmh:oai:open.bu.edu:2144/3064","is_oa":true,"landing_page_url":"https://hdl.handle.net/2144/3064","pdf_url":null,"source":{"id":"https://openalex.org/S4306402183","display_name":"OpenBU/Boston University Institutional Repository (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"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":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2170439","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2170439","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":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-2-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-7","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-7","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2111554887.pdf","grobid_xml":"https://content.openalex.org/works/W2111554887.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1741410789","https://openalex.org/W2099836453","https://openalex.org/W2100412820","https://openalex.org/W2141497252","https://openalex.org/W2149057166","https://openalex.org/W2150297520","https://openalex.org/W2164789250","https://openalex.org/W2611511275","https://openalex.org/W3217097258","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1858249912","https://openalex.org/W2114034199","https://openalex.org/W2317428717","https://openalex.org/W2734259032","https://openalex.org/W4385261515","https://openalex.org/W3094038556","https://openalex.org/W4296345146","https://openalex.org/W2014772881","https://openalex.org/W4254228154","https://openalex.org/W3049477255"],"abstract_inverted_index":{"BACKGROUND:":[0],"Phylogenetic":[1],"trees":[2],"are":[3,92],"widely":[4],"used":[5],"to":[6,40,71,82,87,121],"visualize":[7],"evolutionary":[8],"relationships":[9],"between":[10],"different":[11],"organisms":[12],"or":[13,110],"samples":[14],"of":[15,23,50,77,129],"the":[16,48,75,96,106],"same":[17],"organism.":[18],"There":[19],"exists":[20],"a":[21,57,102,117],"variety":[22],"both":[24],"free":[25],"and":[26,47,63,73,84,104,125,135,141],"commercial":[27],"tree":[28,107],"visualization":[29],"software":[30,68,97],"available,":[31],"but":[32],"limitations":[33],"in":[34,108],"these":[35],"programs":[36,43],"often":[37],"require":[38],"researchers":[39,70,120],"use":[41],"multiple":[42],"for":[44,60,94,119],"analysis,":[45],"annotation,":[46],"production":[49],"publication-ready":[51,127],"images.":[52],"RESULTS:":[53],"We":[54],"present":[55],"TreeViewJ,":[56],"Java":[58],"tool":[59,118],"visualizing,":[61],"editing":[62],"analyzing":[64],"phylogenetic":[65,130],"trees.":[66,131],"The":[67],"allows":[69],"color":[72],"change":[74],"width":[76],"branches":[78],"that":[79],"they":[80],"wish":[81],"highlight,":[83],"add":[85],"names":[86],"nodes.":[88],"If":[89],"collection":[90],"dates":[91],"available":[93,142],"taxa,":[95],"can":[98],"map":[99],"them":[100],"onto":[101],"timeline,":[103],"sort":[105],"ascending":[109],"descending":[111],"date":[112],"order.":[113],"CONCLUSION:":[114],"TreeViewJ":[115],"is":[116,133],"visualize,":[122],"edit,":[123],"\"decorate,\"":[124],"produce":[126],"images":[128],"It":[132],"open-source,":[134],"released":[136],"under":[137],"an":[138],"GPL":[139],"license,":[140],"at":[143],"http://treeviewj.sourceforge.net.":[144]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
