{"id":"https://openalex.org/W1997118774","doi":"https://doi.org/10.1186/1471-2105-11-284","title":"JCoDA: a tool for detecting evolutionary selection","display_name":"JCoDA: a tool for detecting evolutionary selection","publication_year":2010,"publication_date":"2010-05-27","ids":{"openalex":"https://openalex.org/W1997118774","doi":"https://doi.org/10.1186/1471-2105-11-284","mag":"1997118774","pmid":"https://pubmed.ncbi.nlm.nih.gov/20507581"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-284","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-284","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-284","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/10.1186/1471-2105-11-284","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061350674","display_name":"Steven N. Steinway","orcid":"https://orcid.org/0000-0002-4645-293X"},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven N Steinway","raw_affiliation_strings":["Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA","Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628 USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA","institution_ids":["https://openalex.org/I64281891"]},{"raw_affiliation_string":"Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628 USA","institution_ids":["https://openalex.org/I64281891"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062194243","display_name":"Ruth Dannenfelser","orcid":"https://orcid.org/0000-0002-8766-6424"},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruth Dannenfelser","raw_affiliation_strings":["Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA","Dept of Biology, The College of New Jersey, Ewing, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA","institution_ids":["https://openalex.org/I64281891"]},{"raw_affiliation_string":"Dept of Biology, The College of New Jersey, Ewing, USA","institution_ids":["https://openalex.org/I64281891"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035844324","display_name":"Christopher D. Laucius","orcid":null},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher D Laucius","raw_affiliation_strings":["Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA","Dept of Biology, The College of New Jersey, Ewing, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA","institution_ids":["https://openalex.org/I64281891"]},{"raw_affiliation_string":"Dept of Biology, The College of New Jersey, Ewing, USA","institution_ids":["https://openalex.org/I64281891"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007974485","display_name":"James E. Hayes","orcid":"https://orcid.org/0000-0003-1955-8947"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James E Hayes","raw_affiliation_strings":["Weill Cornell Graduate School of Medical Sciences, 1300 York Ave, Box 65, New York, NY, 10065, USA","Weill Cornell Graduate School of Medical Sciences, New York, USA"],"affiliations":[{"raw_affiliation_string":"Weill Cornell Graduate School of Medical Sciences, 1300 York Ave, Box 65, New York, NY, 10065, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Weill Cornell Graduate School of Medical Sciences, New York, USA","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090108448","display_name":"Sudhir Nayak","orcid":null},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudhir Nayak","raw_affiliation_strings":["Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA","Dept of Biology, The College of New Jersey, Ewing, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ, 08628, USA","institution_ids":["https://openalex.org/I64281891"]},{"raw_affiliation_string":"Dept of Biology, The College of New Jersey, Ewing, USA","institution_ids":["https://openalex.org/I64281891"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5061350674"],"corresponding_institution_ids":["https://openalex.org/I64281891"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.4869,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.80715339,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"284","last_page":"284"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9947999715805054,"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/T10487","display_name":"Plant and animal studies","score":0.9922999739646912,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5997776985168457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5393128395080566},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4943690299987793},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4921337962150574},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.48623910546302795},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4741339683532715},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4715585708618164},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45545074343681335},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.42874136567115784},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.41086018085479736},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38633784651756287},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29696816205978394},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2747088074684143},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23294737935066223},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15225157141685486}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5997776985168457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5393128395080566},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4943690299987793},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4921337962150574},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.48623910546302795},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4741339683532715},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4715585708618164},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45545074343681335},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.42874136567115784},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.41086018085479736},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38633784651756287},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29696816205978394},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2747088074684143},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23294737935066223},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15225157141685486},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016415","descriptor_name":"Sequence Alignment","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":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-284","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-284","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-284","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:20507581","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20507581","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:99f90fd4311f40159b1234436a8976b2","is_oa":true,"landing_page_url":"https://doaj.org/article/99f90fd4311f40159b1234436a8976b2","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":"BMC Bioinformatics, Vol 11, Iss 1, p 284 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2887424","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2887424","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-284","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-284","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-284","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/W1997118774.pdf","grobid_xml":"https://content.openalex.org/works/W1997118774.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W81623086","https://openalex.org/W1546639740","https://openalex.org/W1846312500","https://openalex.org/W1907806866","https://openalex.org/W1998139877","https://openalex.org/W2036468098","https://openalex.org/W2044427316","https://openalex.org/W2046183549","https://openalex.org/W2047923658","https://openalex.org/W2073585984","https://openalex.org/W2090415636","https://openalex.org/W2100827887","https://openalex.org/W2104580775","https://openalex.org/W2106882534","https://openalex.org/W2109586979","https://openalex.org/W2110335151","https://openalex.org/W2112697630","https://openalex.org/W2112704704","https://openalex.org/W2113289238","https://openalex.org/W2116111392","https://openalex.org/W2119326915","https://openalex.org/W2120821072","https://openalex.org/W2123200842","https://openalex.org/W2137015675","https://openalex.org/W2137426528","https://openalex.org/W2138468602","https://openalex.org/W2144362290","https://openalex.org/W2148108643","https://openalex.org/W2186908650","https://openalex.org/W3199943451","https://openalex.org/W4205911826","https://openalex.org/W4237033704","https://openalex.org/W4240861547","https://openalex.org/W4247469419"],"related_works":["https://openalex.org/W2156564520","https://openalex.org/W4307843054","https://openalex.org/W2104570606","https://openalex.org/W4210430020","https://openalex.org/W4250611210","https://openalex.org/W4248160505","https://openalex.org/W2048692507","https://openalex.org/W1828108832","https://openalex.org/W2746882944","https://openalex.org/W4290667473"],"abstract_inverted_index":{"JCoDA":[0,17],"is":[1],"a":[2],"configurable,":[3],"open":[4],"source,":[5],"user-friendly":[6],"visualization":[7],"tool":[8],"for":[9,24],"performing":[10],"evolutionary":[11],"analysis":[12],"on":[13],"homologous":[14],"coding":[15],"sequences.":[16],"can":[18,35],"be":[19,36],"used":[20],"to":[21],"rapidly":[22],"screen":[23],"genes":[25,29],"and":[26],"regions":[27],"of":[28],"under":[30],"selection":[31],"using":[32],"PAML.":[33],"It":[34],"freely":[37],"downloaded":[38],"at":[39],"http://www.tcnj.edu/~nayaklab/jcoda.":[40]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
