{"id":"https://openalex.org/W2963672797","doi":"https://doi.org/10.1186/s12859-019-2982-3","title":"JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface","display_name":"JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface","publication_year":2019,"publication_date":"2019-07-22","ids":{"openalex":"https://openalex.org/W2963672797","doi":"https://doi.org/10.1186/s12859-019-2982-3","mag":"2963672797","pmid":"https://pubmed.ncbi.nlm.nih.gov/31331268"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2982-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2982-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2982-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2982-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042952708","display_name":"Ben C St\u00f6ver","orcid":"https://orcid.org/0000-0003-4443-7733"},"institutions":[{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ben C. St\u00f6ver","raw_affiliation_strings":["Institute for Evolution and Biodiversity, WWU M\u00fcnster, H\u00fcfferstra\u00dfe 1, 48149, M\u00fcnster, Germany. stoever@bioinfweb.info","Institute for Evolution and Biodiversity, WWU M\u00fcnster, M\u00fcnster, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4443-7733","affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, WWU M\u00fcnster, H\u00fcfferstra\u00dfe 1, 48149, M\u00fcnster, Germany. stoever@bioinfweb.info","institution_ids":["https://openalex.org/I4210096541"]},{"raw_affiliation_string":"Institute for Evolution and Biodiversity, WWU M\u00fcnster, M\u00fcnster, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043109034","display_name":"Sarah Wiechers","orcid":"https://orcid.org/0000-0002-3899-3461"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]},{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sarah Wiechers","raw_affiliation_strings":["Institute for Evolution and Biodiversity, WWU M\u00fcnster, H\u00fcfferstra\u00dfe 1, 48149, M\u00fcnster, Germany","Institute for Evolution and Biodiversity, WWU M\u00fcnster, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, WWU M\u00fcnster, H\u00fcfferstra\u00dfe 1, 48149, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464","https://openalex.org/I4210096541"]},{"raw_affiliation_string":"Institute for Evolution and Biodiversity, WWU M\u00fcnster, M\u00fcnster, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053484497","display_name":"Kai M\u00fcller","orcid":"https://orcid.org/0000-0002-0962-3824"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]},{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kai F. M\u00fcller","raw_affiliation_strings":["Institute for Evolution and Biodiversity, WWU M\u00fcnster, H\u00fcfferstra\u00dfe 1, 48149, M\u00fcnster, Germany","Institute for Evolution and Biodiversity, WWU M\u00fcnster, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, WWU M\u00fcnster, H\u00fcfferstra\u00dfe 1, 48149, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464","https://openalex.org/I4210096541"]},{"raw_affiliation_string":"Institute for Evolution and Biodiversity, WWU M\u00fcnster, M\u00fcnster, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5042952708"],"corresponding_institution_ids":["https://openalex.org/I4210096541"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":1573,"currency":"EUR","value_usd":1696},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05588606,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"20","issue":"1","first_page":"402","last_page":"402"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5821999907493591,"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":0.5821999907493591,"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":0.07020000368356705,"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"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0608999989926815,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8817867636680603},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.7180884480476379},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5524239540100098},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5329656600952148},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5157316327095032},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5149248838424683},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.49798107147216797},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4605950117111206},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4506825804710388},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.4473792016506195},{"id":"https://openalex.org/keywords/metadata-repository","display_name":"Metadata repository","score":0.4294835925102234},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4269537925720215},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.41153091192245483},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.330757200717926},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3275061249732971},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2794496715068817},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18017059564590454},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09930595755577087}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8817867636680603},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7180884480476379},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5524239540100098},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5329656600952148},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5157316327095032},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5149248838424683},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.49798107147216797},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4605950117111206},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4506825804710388},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.4473792016506195},{"id":"https://openalex.org/C153048206","wikidata":"https://www.wikidata.org/wiki/Q3454922","display_name":"Metadata repository","level":3,"score":0.4294835925102234},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4269537925720215},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.41153091192245483},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.330757200717926},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3275061249732971},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2794496715068817},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18017059564590454},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09930595755577087},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-2982-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2982-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2982-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31331268","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31331268","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:9048c051536c4908a4f5452bfe156aa2","is_oa":true,"landing_page_url":"https://doaj.org/article/9048c051536c4908a4f5452bfe156aa2","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-15 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6647125","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6647125","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:wwu.de:3279a6ac-89ca-4017-8322-2dcf1e69f496","is_oa":true,"landing_page_url":"https://nbn-resolving.org/urn:nbn:de:hbz:6-99039422874","pdf_url":null,"source":{"id":"https://openalex.org/S4306402051","display_name":"URN:NBN Resolver for Germany & Switzerland (German National Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2802635041","host_organization_name":"Technische Informationsbibliothek (TIB)","host_organization_lineage":["https://openalex.org/I2802635041"],"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":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2982-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2982-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2982-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.800000011920929,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2871439716","display_name":null,"funder_award_id":"MU 2875/3-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2963672797.pdf","grobid_xml":"https://content.openalex.org/works/W2963672797.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1649645444","https://openalex.org/W1967649545","https://openalex.org/W1973576398","https://openalex.org/W1975957527","https://openalex.org/W2012358566","https://openalex.org/W2018368579","https://openalex.org/W2024986130","https://openalex.org/W2026062398","https://openalex.org/W2036318837","https://openalex.org/W2050529257","https://openalex.org/W2060527586","https://openalex.org/W2065939324","https://openalex.org/W2097734528","https://openalex.org/W2100412820","https://openalex.org/W2100704846","https://openalex.org/W2100827887","https://openalex.org/W2101654334","https://openalex.org/W2105803236","https://openalex.org/W2111946420","https://openalex.org/W2120337732","https://openalex.org/W2120375049","https://openalex.org/W2121251817","https://openalex.org/W2132247062","https://openalex.org/W2133855669","https://openalex.org/W2134415959","https://openalex.org/W2139736670","https://openalex.org/W2139995546","https://openalex.org/W2142678031","https://openalex.org/W2143176024","https://openalex.org/W2145252923","https://openalex.org/W2148698435","https://openalex.org/W2148916226","https://openalex.org/W2149057166","https://openalex.org/W2150838945","https://openalex.org/W2150934173","https://openalex.org/W2152207030","https://openalex.org/W2156689933","https://openalex.org/W2160377812","https://openalex.org/W2164306581","https://openalex.org/W2166432938","https://openalex.org/W2169231369","https://openalex.org/W2170041483","https://openalex.org/W2170057885","https://openalex.org/W2260720483","https://openalex.org/W2298562014","https://openalex.org/W2299597245","https://openalex.org/W2311203695","https://openalex.org/W2536735827","https://openalex.org/W2575354493","https://openalex.org/W2604308930","https://openalex.org/W2611511275","https://openalex.org/W2617703913","https://openalex.org/W2761744647","https://openalex.org/W2795697644","https://openalex.org/W2951002538","https://openalex.org/W3121953277"],"related_works":["https://openalex.org/W1552553528","https://openalex.org/W2183628870","https://openalex.org/W3023161639","https://openalex.org/W2008531296","https://openalex.org/W2782431616","https://openalex.org/W2379265733","https://openalex.org/W2394393789","https://openalex.org/W2374379029","https://openalex.org/W1503116306","https://openalex.org/W4299935056"],"abstract_inverted_index":{"BACKGROUND:":[0],"Today":[1],"a":[2,43,161],"variety":[3],"of":[4,10,91,99,109,114,138,153,172,233,237,264],"phylogenetic":[5,254],"file":[6],"formats":[7,41,94,244,268],"exists,":[8],"some":[9],"which":[11,132],"are":[12],"well-established":[13],"but":[14],"limited":[15,44],"in":[16,101,224],"their":[17,225],"data":[18,68,87,187],"model,":[19,46],"while":[20],"other":[21],"more":[22,56,265],"recently":[23],"introduced":[24],"ones":[25],"offer":[26],"advanced":[27,57],"features":[28,152,223],"for":[29,54,62,121,193,215],"metadata":[30,45,89,123],"representation.":[31],"Although":[32],"most":[33,140],"currently":[34,156],"available":[35],"software":[36,116,255],"only":[37],"supports":[38],"the":[39,55,86,92,107,112,119,128,139,154,177,212,248,259],"classical":[40],"with":[42,184],"it":[47],"would":[48,104],"be":[49,71,182],"desirable":[50],"to":[51,64,117,150,176,219,250],"have":[52],"support":[53,170,241],"formats.":[58,145,158,174],"This":[59,246],"is":[60,190,197],"necessary":[61],"users":[63],"produce":[65],"richly":[66],"annotated":[67],"that":[69,83,240],"can":[70,169,181],"efficiently":[72],"reused":[73],"and":[74,88,95,111,136,143,165,189,203,235,257],"make":[75],"underlying":[76],"workflows":[77],"easily":[78],"reproducible.":[79],"A":[80],"programming":[81],"library":[82,130],"abstracts":[84],"over":[85],"models":[90],"different":[93],"allows":[96,133,147],"supporting":[97],"all":[98,151,171],"them":[100],"one":[102],"step":[103],"significantly":[105,210],"simplify":[106],"development":[108,232],"new":[110,234],"extension":[113,236],"existing":[115,238],"address":[118],"need":[120],"better":[122],"annotation.":[124],"RESULTS:":[125],"We":[126],"developed":[127],"Java":[129],"JPhyloIO,":[131],"event-based":[134,178],"reading":[135],"writing":[137],"common":[141],"alignment":[142],"tree/network":[144],"It":[146],"full":[148],"access":[149],"nine":[155],"supported":[157],"By":[159],"implementing":[160],"single":[162],"JPhyloIO-based":[163],"reader":[164],"writer,":[166],"application":[167,186],"developers":[168],"these":[173],"Due":[175],"architecture,":[179],"JPhyloIO":[180,196,229],"combined":[183],"any":[185],"structure,":[188],"memory":[191],"efficient":[192],"large":[194],"datasets.":[195],"distributed":[198],"under":[199],"LGPL.":[200],"Detailed":[201],"documentation":[202],"example":[204],"applications":[205,239],"(available":[206],"on":[207],"http://bioinfweb.info/JPhyloIO/":[208],")":[209],"lower":[211],"entry":[213],"barrier":[214],"bioinformaticians":[216],"who":[217],"wish":[218],"benefit":[220],"from":[221],"JPhyloIO's":[222],"own":[226],"software.":[227],"CONCLUSION:":[228],"enables":[230],"simplified":[231],"various":[242],"standard":[243],"simultaneously.":[245],"has":[247],"potential":[249],"improve":[251],"interoperability":[252],"between":[253],"tools":[256],"at":[258],"same":[260],"time":[261],"motivate":[262],"usage":[263],"recent":[266],"metadata-rich":[267],"such":[269],"as":[270],"NeXML":[271],"or":[272],"phyloXML.":[273]},"counts_by_year":[],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
