{"id":"https://openalex.org/W2149557149","doi":"https://doi.org/10.1093/bioinformatics/btm619","title":"Phyutility: a phyloinformatics tool for trees, alignments and molecular data","display_name":"Phyutility: a phyloinformatics tool for trees, alignments and molecular data","publication_year":2008,"publication_date":"2008-01-28","ids":{"openalex":"https://openalex.org/W2149557149","doi":"https://doi.org/10.1093/bioinformatics/btm619","mag":"2149557149","pmid":"https://pubmed.ncbi.nlm.nih.gov/18227120"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm619","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm619","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/715/49052195/bioinformatics_24_5_715.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,"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/715/49052195/bioinformatics_24_5_715.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019827410","display_name":"Stephen A. Smith","orcid":"https://orcid.org/0000-0003-2035-9531"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen A. Smith","raw_affiliation_strings":["1 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520 and 2Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520 and 2Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA","institution_ids":["https://openalex.org/I32971472","https://openalex.org/I27804330"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068691883","display_name":"Casey W. Dunn","orcid":"https://orcid.org/0000-0003-0628-5150"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Casey W. Dunn","raw_affiliation_strings":["1 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520 and 2Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520 and 2Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA","institution_ids":["https://openalex.org/I32971472","https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5019827410"],"corresponding_institution_ids":["https://openalex.org/I27804330","https://openalex.org/I32971472"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":9.6814,"has_fulltext":true,"cited_by_count":672,"citation_normalized_percentile":{"value":0.98726631,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"5","first_page":"715","last_page":"716"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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":0.9988999962806702,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9968000054359436,"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"}},{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.9894000291824341,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.9284555912017822},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.778670072555542},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.7121082544326782},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5793004631996155},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5725342035293579},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5720469951629639},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5335196852684021},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5140300989151001},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4851192235946655},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4207318425178528},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3934503495693207},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3585188388824463},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32438400387763977},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15980425477027893},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10485240817070007}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.9284555912017822},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.778670072555542},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.7121082544326782},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5793004631996155},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5725342035293579},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5720469951629639},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5335196852684021},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5140300989151001},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4851192235946655},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4207318425178528},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3934503495693207},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3585188388824463},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32438400387763977},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15980425477027893},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10485240817070007},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","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/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm619","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm619","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/715/49052195/bioinformatics_24_5_715.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,"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:18227120","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18227120","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm619","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm619","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/715/49052195/bioinformatics_24_5_715.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,"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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149557149.pdf","grobid_xml":"https://content.openalex.org/works/W2149557149.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1963957860","https://openalex.org/W1983792126","https://openalex.org/W2064376895","https://openalex.org/W2127474816","https://openalex.org/W2132179631","https://openalex.org/W2132926880","https://openalex.org/W2146058063"],"related_works":["https://openalex.org/W2350278424","https://openalex.org/W2071432835","https://openalex.org/W4234371507","https://openalex.org/W4299534542","https://openalex.org/W2598672065","https://openalex.org/W3120610872","https://openalex.org/W1638297612","https://openalex.org/W1602159133","https://openalex.org/W2523911541","https://openalex.org/W3081644756"],"abstract_inverted_index":{"Phyutility,":[0],"including":[1],"source":[2],"code,":[3],"documentation,":[4],"examples,":[5],"and":[6],"executables,":[7],"is":[8],"available":[9],"at":[10],"http://code.google.com/p/phyutility.":[11]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":45},{"year":2024,"cited_by_count":42},{"year":2023,"cited_by_count":38},{"year":2022,"cited_by_count":39},{"year":2021,"cited_by_count":98},{"year":2020,"cited_by_count":71},{"year":2019,"cited_by_count":48},{"year":2018,"cited_by_count":30},{"year":2017,"cited_by_count":28},{"year":2016,"cited_by_count":41},{"year":2015,"cited_by_count":36},{"year":2014,"cited_by_count":44},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":20}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}