{"id":"https://openalex.org/W2137015563","doi":"https://doi.org/10.1186/1748-7188-7-8","title":"Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots","display_name":"Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots","publication_year":2012,"publication_date":"2012-05-02","ids":{"openalex":"https://openalex.org/W2137015563","doi":"https://doi.org/10.1186/1748-7188-7-8","mag":"2137015563","pmid":"https://pubmed.ncbi.nlm.nih.gov/22549005"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-7-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-7-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-7-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-7-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084752404","display_name":"F. A. Matsen","orcid":"https://orcid.org/0000-0003-0607-6025"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Frederick A Matsen","raw_affiliation_strings":["Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. matsen@fhcrc.org","Fred Hutchinson Cancer Research Center, Seattle, USA"],"affiliations":[{"raw_affiliation_string":"Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. matsen@fhcrc.org","institution_ids":[]},{"raw_affiliation_string":"Fred Hutchinson Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076585627","display_name":"Aaron Gallagher","orcid":null},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Gallagher","raw_affiliation_strings":["Fred Hutchinson Cancer Research Center, Seattle, Washington, USA","Fred Hutchinson Cancer Research Center, Seattle, USA"],"affiliations":[{"raw_affiliation_string":"Fred Hutchinson Cancer Research Center, Seattle, Washington, USA","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Fred Hutchinson Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084752404"],"corresponding_institution_ids":["https://openalex.org/I4210089486"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":1.2102,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.78490326,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"7","issue":"1","first_page":"8","last_page":"8"},"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":0.9983000159263611,"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":0.9932000041007996,"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":0.7112712860107422},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6597175598144531},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5800684094429016},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5651700496673584},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.561296284198761},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.5182135701179504},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4566475749015808},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.41837871074676514},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33301499485969543},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21996453404426575},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19012638926506042},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08109873533248901}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7112712860107422},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6597175598144531},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5800684094429016},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5651700496673584},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.561296284198761},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.5182135701179504},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4566475749015808},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.41837871074676514},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33301499485969543},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21996453404426575},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19012638926506042},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08109873533248901},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"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/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","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":4,"locations":[{"id":"doi:10.1186/1748-7188-7-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-7-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-7-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:22549005","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22549005","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:1d8bf20ddbe5405d9deefd64c377cf98","is_oa":true,"landing_page_url":"https://doaj.org/article/1d8bf20ddbe5405d9deefd64c377cf98","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 7, Iss 1, p 8 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2388926","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3384453","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-7-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-7-8","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-7-8","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1832083476","display_name":null,"funder_award_id":"HG005966-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"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/W2137015563.pdf","grobid_xml":"https://content.openalex.org/works/W2137015563.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1504929631","https://openalex.org/W1617085997","https://openalex.org/W1989175238","https://openalex.org/W2029029999","https://openalex.org/W2031611770","https://openalex.org/W2047715328","https://openalex.org/W2111929782","https://openalex.org/W2154026962","https://openalex.org/W2155606054","https://openalex.org/W2156856635","https://openalex.org/W2168696662","https://openalex.org/W2276499310","https://openalex.org/W2335915014","https://openalex.org/W2561728979"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2883025420","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W1974895455"],"abstract_inverted_index":{"The":[0],"algorithms":[1],"in":[2],"this":[3],"paper,":[4],"and":[5,15],"the":[6],"associated":[7],"freely-available":[8],"software,":[9],"will":[10],"help":[11],"biologists":[12],"better":[13],"use":[14],"understand":[16],"taxonomically":[17],"labeled":[18],"phylogenetic":[19],"trees.":[20]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
