{"id":"https://openalex.org/W3126870464","doi":"https://doi.org/10.1093/bioinformatics/btab096","title":"PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data","display_name":"PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data","publication_year":2021,"publication_date":"2021-02-05","ids":{"openalex":"https://openalex.org/W3126870464","doi":"https://doi.org/10.1093/bioinformatics/btab096","mag":"3126870464","pmid":"https://pubmed.ncbi.nlm.nih.gov/33560364"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab096","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab096","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8388027","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071152958","display_name":"Jacob L. Steenwyk","orcid":"https://orcid.org/0000-0002-8436-595X"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jacob L Steenwyk","raw_affiliation_strings":["Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065496237","display_name":"Thomas J. Buida","orcid":"https://orcid.org/0000-0001-9367-6189"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thomas J Buida","raw_affiliation_strings":["9 City Place #312, Nashville , TN 37209, USA"],"affiliations":[{"raw_affiliation_string":"9 City Place #312, Nashville , TN 37209, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074859011","display_name":"Abigail L. LaBella","orcid":"https://orcid.org/0000-0003-0068-6703"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abigail L Labella","raw_affiliation_strings":["Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000168074","display_name":"Yuanning Li","orcid":"https://orcid.org/0000-0002-2206-5804"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuanning Li","raw_affiliation_strings":["Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076622760","display_name":"Xing\u2010Xing Shen","orcid":"https://orcid.org/0000-0001-5765-1419"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xing-Xing Shen","raw_affiliation_strings":["Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China"],"affiliations":[{"raw_affiliation_string":"Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046883178","display_name":"Antonis Rokas","orcid":"https://orcid.org/0000-0002-7248-6551"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Antonis Rokas","raw_affiliation_strings":["Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Vanderbilt University , VU Station B #35-1634, Nashville, TN 37235, USA","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046883178","https://openalex.org/A5071152958"],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":11.8755,"has_fulltext":false,"cited_by_count":215,"citation_normalized_percentile":{"value":0.99271891,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"37","issue":"16","first_page":"2325","last_page":"2331"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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":0.9970999956130981,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"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/computer-science","display_name":"Computer science","score":0.7318006157875061},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.6671167612075806},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5999006628990173},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5685384273529053},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5451890230178833},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.5155882239341736},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.49590858817100525},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48690927028656006},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4442577064037323},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4244655966758728},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32038652896881104},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.27544140815734863},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.252277135848999},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18390443921089172},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1593123972415924},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.15300434827804565}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7318006157875061},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.6671167612075806},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5999006628990173},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5685384273529053},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5451890230178833},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.5155882239341736},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.49590858817100525},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48690927028656006},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4442577064037323},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4244655966758728},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32038652896881104},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.27544140815734863},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.252277135848999},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18390443921089172},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1593123972415924},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.15300434827804565},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab096","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab096","pdf_url":null,"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:33560364","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33560364","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},{"id":"pmh:oai:pubmedcentral.nih.gov:8388027","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8388027","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8388027","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8388027","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1765970067","display_name":null,"funder_award_id":"32071665","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7809628153","display_name":null,"funder_award_id":"2020QNA6019","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":75,"referenced_works":["https://openalex.org/W1605984840","https://openalex.org/W1966446749","https://openalex.org/W1966972227","https://openalex.org/W1974736523","https://openalex.org/W1980690176","https://openalex.org/W1988622898","https://openalex.org/W2012220164","https://openalex.org/W2024420148","https://openalex.org/W2046183549","https://openalex.org/W2052184658","https://openalex.org/W2052668637","https://openalex.org/W2060425093","https://openalex.org/W2071467238","https://openalex.org/W2090427748","https://openalex.org/W2101896427","https://openalex.org/W2110912468","https://openalex.org/W2111414304","https://openalex.org/W2112504441","https://openalex.org/W2114850508","https://openalex.org/W2119837484","https://openalex.org/W2121053101","https://openalex.org/W2125867054","https://openalex.org/W2129589314","https://openalex.org/W2130198181","https://openalex.org/W2131531207","https://openalex.org/W2140400782","https://openalex.org/W2147838733","https://openalex.org/W2148860972","https://openalex.org/W2151409320","https://openalex.org/W2152568394","https://openalex.org/W2157701114","https://openalex.org/W2161724899","https://openalex.org/W2162000763","https://openalex.org/W2162448519","https://openalex.org/W2172696783","https://openalex.org/W2174364811","https://openalex.org/W2272393905","https://openalex.org/W2277953252","https://openalex.org/W2311203695","https://openalex.org/W2326227609","https://openalex.org/W2342591163","https://openalex.org/W2465050739","https://openalex.org/W2487115603","https://openalex.org/W2506408709","https://openalex.org/W2513727910","https://openalex.org/W2528315574","https://openalex.org/W2570931575","https://openalex.org/W2586193102","https://openalex.org/W2740354071","https://openalex.org/W2747131829","https://openalex.org/W2755331695","https://openalex.org/W2766641567","https://openalex.org/W2790050774","https://openalex.org/W2794847726","https://openalex.org/W2801361050","https://openalex.org/W2804058466","https://openalex.org/W2899763402","https://openalex.org/W2956842353","https://openalex.org/W2957892651","https://openalex.org/W2972858953","https://openalex.org/W2976065467","https://openalex.org/W2981543307","https://openalex.org/W2982255935","https://openalex.org/W3003257820","https://openalex.org/W3025857586","https://openalex.org/W3080850168","https://openalex.org/W3096491883","https://openalex.org/W3103145119","https://openalex.org/W3107541694","https://openalex.org/W4253068584","https://openalex.org/W4256288253","https://openalex.org/W6685415645","https://openalex.org/W6704380114","https://openalex.org/W6743072547","https://openalex.org/W6781878624"],"related_works":["https://openalex.org/W2380915035","https://openalex.org/W2057191541","https://openalex.org/W2150471837","https://openalex.org/W4242650659","https://openalex.org/W2362218761","https://openalex.org/W2113708670","https://openalex.org/W2099352317","https://openalex.org/W2062354928","https://openalex.org/W2088120817","https://openalex.org/W2158340599"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":61},{"year":2024,"cited_by_count":68},{"year":2023,"cited_by_count":43},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
