{"id":"https://openalex.org/W2097734528","doi":"https://doi.org/10.1186/1471-2105-9-532","title":"Extended Newick: it is time for a standard representation of phylogenetic networks","display_name":"Extended Newick: it is time for a standard representation of phylogenetic networks","publication_year":2008,"publication_date":"2008-12-01","ids":{"openalex":"https://openalex.org/W2097734528","doi":"https://doi.org/10.1186/1471-2105-9-532","mag":"2097734528","pmid":"https://pubmed.ncbi.nlm.nih.gov/19077301"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-532","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-532","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-532","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/counter/pdf/10.1186/1471-2105-9-532","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006561727","display_name":"Gabriel Cardona","orcid":"https://orcid.org/0000-0001-8845-4290"},"institutions":[{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gabriel Cardona","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Spain. gabriel.cardona@uib.es","Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, Spain. gabriel.cardona@uib.es","institution_ids":["https://openalex.org/I50441567"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087466847","display_name":"Francesc Rossell\u00f3","orcid":"https://orcid.org/0000-0003-2897-5398"},"institutions":[{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francesc Rossell\u00f3","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122, Palma de Mallorca, Spain","Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122, Palma de Mallorca, Spain","institution_ids":["https://openalex.org/I50441567"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005629452","display_name":"Gabriel Valiente","orcid":"https://orcid.org/0000-0001-9194-2703"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Gabriel Valiente","raw_affiliation_strings":["Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain","Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006561727"],"corresponding_institution_ids":["https://openalex.org/I50441567"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9654,"has_fulltext":true,"cited_by_count":120,"citation_normalized_percentile":{"value":0.74878873,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"532","last_page":"532"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9966999888420105,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.9197207689285278},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.8922523260116577},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.48139241337776184},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.480969101190567},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.45524686574935913},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40712183713912964},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.405693382024765},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38857951760292053},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.335917592048645},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15431511402130127},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15403082966804504},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10069873929023743}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.9197207689285278},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.8922523260116577},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.48139241337776184},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.480969101190567},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.45524686574935913},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40712183713912964},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.405693382024765},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38857951760292053},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.335917592048645},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15431511402130127},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15403082966804504},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10069873929023743},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D006824","descriptor_name":"Hybridization, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006824","descriptor_name":"Hybridization, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006824","descriptor_name":"Hybridization, Genetic","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":"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":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-532","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-532","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-532","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:19077301","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19077301","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:7745f545668e48f6bea464027750fe91","is_oa":true,"landing_page_url":"https://doaj.org/article/7745f545668e48f6bea464027750fe91","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 532 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2621367","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2621367","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-532","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-532","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-532","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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2097734528.pdf","grobid_xml":"https://content.openalex.org/works/W2097734528.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1497135357","https://openalex.org/W1975957527","https://openalex.org/W2013134176","https://openalex.org/W2043710019","https://openalex.org/W2055298722","https://openalex.org/W2072522782","https://openalex.org/W2078151980","https://openalex.org/W2097243089","https://openalex.org/W2110263284","https://openalex.org/W2115638597","https://openalex.org/W2117077912","https://openalex.org/W2118780696","https://openalex.org/W2128140984","https://openalex.org/W2150934173","https://openalex.org/W2164418313","https://openalex.org/W2259225862","https://openalex.org/W4233815609"],"related_works":["https://openalex.org/W4254268221","https://openalex.org/W2951650999","https://openalex.org/W2038264393","https://openalex.org/W147282674","https://openalex.org/W2112400707","https://openalex.org/W4300585845","https://openalex.org/W2101991559","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2057191541"],"abstract_inverted_index":{"The":[0],"adoption":[1],"of":[2,13,23,37],"the":[3,11,21],"extended":[4],"Newick":[5],"format":[6],"as":[7],"a":[8,34],"standard":[9],"for":[10],"representation":[12],"phylogenetic":[14,25,39],"network":[15],"is":[16],"an":[17],"important":[18],"step":[19],"towards":[20],"publication":[22],"explicit":[24],"networks":[26],"in":[27,33],"peer-reviewed":[28],"journals":[29],"and":[30],"their":[31],"incorporation":[32],"future":[35],"database":[36],"published":[38],"networks.":[40]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":4}],"updated_date":"2026-03-29T08:15:47.926485","created_date":"2025-10-10T00:00:00"}
