{"id":"https://openalex.org/W2155670229","doi":"https://doi.org/10.1093/bioinformatics/btt009","title":"gKaKs: the pipeline for genome-level Ka/Ks calculation","display_name":"gKaKs: the pipeline for genome-level Ka/Ks calculation","publication_year":2013,"publication_date":"2013-01-12","ids":{"openalex":"https://openalex.org/W2155670229","doi":"https://doi.org/10.1093/bioinformatics/btt009","mag":"2155670229","pmid":"https://pubmed.ncbi.nlm.nih.gov/23314322"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/645/50335809/bioinformatics_29_5_645.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/29/5/645/50335809/bioinformatics_29_5_645.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100777284","display_name":"Chengjun Zhang","orcid":"https://orcid.org/0000-0001-9759-4906"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chengjun Zhang","raw_affiliation_strings":["1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA","institution_ids":["https://openalex.org/I185443292","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111964102","display_name":"Jun Wang","orcid":"https://orcid.org/0009-0008-8475-2934"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA","institution_ids":["https://openalex.org/I185443292","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037432233","display_name":"Manyuan Long","orcid":"https://orcid.org/0000-0002-6755-197X"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manyuan Long","raw_affiliation_strings":["1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA","institution_ids":["https://openalex.org/I185443292","https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084814231","display_name":"Chuanzhu Fan","orcid":"https://orcid.org/0000-0002-1842-4560"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chuanzhu Fan","raw_affiliation_strings":["1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 and 2Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA","institution_ids":["https://openalex.org/I185443292","https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5084814231"],"corresponding_institution_ids":["https://openalex.org/I185443292","https://openalex.org/I40347166"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3807,"has_fulltext":false,"cited_by_count":52,"citation_normalized_percentile":{"value":0.89074263,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"5","first_page":"645","last_page":"646"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.995199978351593,"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/perl","display_name":"Perl","score":0.7744051218032837},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7606194019317627},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49923133850097656},{"id":"https://openalex.org/keywords/substitution","display_name":"Substitution (logic)","score":0.4776122272014618},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47446542978286743},{"id":"https://openalex.org/keywords/frameshift-mutation","display_name":"Frameshift mutation","score":0.44129934906959534},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4257122576236725},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34295654296875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3262483775615692},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.18048521876335144},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1036565899848938}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.7744051218032837},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7606194019317627},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49923133850097656},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.4776122272014618},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47446542978286743},{"id":"https://openalex.org/C29906990","wikidata":"https://www.wikidata.org/wiki/Q1440688","display_name":"Frameshift mutation","level":4,"score":0.44129934906959534},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4257122576236725},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34295654296875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3262483775615692},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.18048521876335144},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1036565899848938}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D016368","descriptor_name":"Frameshift Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016368","descriptor_name":"Frameshift Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016368","descriptor_name":"Frameshift Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/645/50335809/bioinformatics_29_5_645.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:23314322","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23314322","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/btt009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/645/50335809/bioinformatics_29_5_645.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"},{"id":"https://openalex.org/F4320309272","display_name":"Wayne State University","ror":"https://ror.org/01070mq45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155670229.pdf","grobid_xml":"https://content.openalex.org/works/W2155670229.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1881907338","https://openalex.org/W1907806866","https://openalex.org/W1920973730","https://openalex.org/W1988652743","https://openalex.org/W2003062832","https://openalex.org/W2035454907","https://openalex.org/W2046183549","https://openalex.org/W2055043387","https://openalex.org/W2085950302","https://openalex.org/W2104306559","https://openalex.org/W2110335151","https://openalex.org/W2129775611","https://openalex.org/W2131413085","https://openalex.org/W2131505046","https://openalex.org/W2136145671","https://openalex.org/W2136872570","https://openalex.org/W2150934173","https://openalex.org/W2157600799","https://openalex.org/W4293196852","https://openalex.org/W6639969845","https://openalex.org/W6640287769","https://openalex.org/W6675831761","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W2480056510","https://openalex.org/W2412623563","https://openalex.org/W190299232","https://openalex.org/W1521481095","https://openalex.org/W594361471","https://openalex.org/W2604964690","https://openalex.org/W2417897055","https://openalex.org/W2613359208","https://openalex.org/W2291334382","https://openalex.org/W4207058155"],"abstract_inverted_index":{"gKaKs":[0],"is":[1,6,15],"implemented":[2],"in":[3],"Perl":[4],"and":[5],"freely":[7],"available":[8,16],"on":[9,17],"http://longlab.uchicago.edu/?q=gKaKs.":[10],"The":[11],"detailed":[12],"user":[13],"manual":[14],"the":[18],"website.":[19]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
