{"id":"https://openalex.org/W2024790961","doi":"https://doi.org/10.1093/bioinformatics/btn057","title":"Tracing evolutionary pressure","display_name":"Tracing evolutionary pressure","publication_year":2008,"publication_date":"2008-02-26","ids":{"openalex":"https://openalex.org/W2024790961","doi":"https://doi.org/10.1093/bioinformatics/btn057","mag":"2024790961","pmid":"https://pubmed.ncbi.nlm.nih.gov/18304936"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn057","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/908/49047072/bioinformatics_24_7_908.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/24/7/908/49047072/bioinformatics_24_7_908.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032548139","display_name":"Kai Ye","orcid":"https://orcid.org/0000-0002-2851-6741"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Kai Ye","raw_affiliation_strings":["1 Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden and 2CMBI, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden and 2CMBI, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I121797337","https://openalex.org/I145872427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075419050","display_name":"Gert Vriend","orcid":"https://orcid.org/0000-0002-1067-7053"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Gert Vriend","raw_affiliation_strings":["1 Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden and 2CMBI, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden and 2CMBI, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I121797337","https://openalex.org/I145872427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065525958","display_name":"Adriaan P. IJzerman","orcid":"https://orcid.org/0000-0002-1182-2259"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Adriaan P. IJzerman","raw_affiliation_strings":["1 Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden and 2CMBI, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden and 2CMBI, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I121797337","https://openalex.org/I145872427"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5032548139"],"corresponding_institution_ids":["https://openalex.org/I121797337","https://openalex.org/I145872427"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.5931,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.82071282,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"7","first_page":"908","last_page":"915"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9925000071525574,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9829999804496765,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8107564449310303},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5980453491210938},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5556530356407166},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.500924825668335},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49936771392822266},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44703853130340576},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.43151354789733887},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4314473271369934},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39671438932418823},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36617153882980347},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.351290225982666},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3281363844871521},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26981139183044434},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.22142186760902405},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14818736910820007},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11329647898674011}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8107564449310303},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5980453491210938},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5556530356407166},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.500924825668335},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49936771392822266},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44703853130340576},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.43151354789733887},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4314473271369934},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39671438932418823},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36617153882980347},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.351290225982666},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3281363844871521},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26981139183044434},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.22142186760902405},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14818736910820007},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11329647898674011},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn057","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/908/49047072/bioinformatics_24_7_908.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:18304936","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18304936","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":"Journal Article"},{"id":"pmh:oai:repository.ubn.ru.nl:2066/70580","is_oa":false,"landing_page_url":"http://hdl.handle.net/2066/70580","pdf_url":null,"source":{"id":"https://openalex.org/S4306401067","display_name":"Radboud Repository (Radboud University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I145872427","host_organization_name":"Radboud University Nijmegen","host_organization_lineage":["https://openalex.org/I145872427"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 24, 7, pp. 908-15","raw_type":"Article / Letter to editor"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn057","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/908/49047072/bioinformatics_24_7_908.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":[{"id":"https://metadata.un.org/sdg/15","score":0.5699999928474426,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2024790961.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W124504601","https://openalex.org/W1510818199","https://openalex.org/W1965582988","https://openalex.org/W1966985448","https://openalex.org/W1975493488","https://openalex.org/W1975563330","https://openalex.org/W1982481323","https://openalex.org/W1990291472","https://openalex.org/W1994261741","https://openalex.org/W2000137866","https://openalex.org/W2005393972","https://openalex.org/W2010260387","https://openalex.org/W2069663555","https://openalex.org/W2073110681","https://openalex.org/W2085075228","https://openalex.org/W2094476260","https://openalex.org/W2098822872","https://openalex.org/W2098830117","https://openalex.org/W2104572985","https://openalex.org/W2110411872","https://openalex.org/W2117249420","https://openalex.org/W2117384673","https://openalex.org/W2119692371","https://openalex.org/W2128478556","https://openalex.org/W2133978245","https://openalex.org/W2139919097","https://openalex.org/W2141885858","https://openalex.org/W2143630321","https://openalex.org/W2145088375","https://openalex.org/W2146396346","https://openalex.org/W2155469822","https://openalex.org/W2158772300","https://openalex.org/W2163105490","https://openalex.org/W2163352757","https://openalex.org/W2169830295","https://openalex.org/W2329156357","https://openalex.org/W2417710273","https://openalex.org/W4210400672","https://openalex.org/W4233523656","https://openalex.org/W7074130324"],"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/W2746882944","https://openalex.org/W2314370104"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"advances":[2],"in":[3,135,237,268,278,283,294],"sequencing":[4],"techniques":[5],"have":[6,53],"yielded":[7],"enormous":[8],"amounts":[9],"of":[10,39,102,113,120,131,162,169,181,195,221,234],"protein":[11,104,239,254],"sequence":[12,21,64],"data":[13],"from":[14,61,156,191],"various":[15,247],"species.":[16],"This":[17,226],"large":[18],"dataset":[19],"allows":[20,229],"comparison":[22],"between":[23],"paralogous":[24],"and":[25,48,83,252,273,291],"orthologous":[26],"proteins":[27],"to":[28,56,71,137,151,159,177,197,204,215,265],"identify":[29],"motifs":[30],"or":[31,210,218],"functional":[32,40],"positions":[33,60,87,277],"that":[34,206,259],"account":[35],"for":[36,301],"the":[37,49,99,108,114,118,124,153,157,160,163,170,179,182,192,216,222,279,284],"differences":[38,267],"subgroups":[41],"('specificity'":[42],"positions).":[43],"Algorithms":[44],"such":[45,58,77],"as":[46,78],"SDPpred":[47],"two-entropies":[50],"analysis":[51,233],"(TEA)":[52],"been":[54],"developed":[55],"detect":[57],"specificity":[59,86,121,139],"a":[62,81,103,145,172,199,238],"multiple":[63],"alignment":[65],"(MSA)":[66],"grouped":[67],"into":[68],"classes":[69],"according":[70],"certain":[72],"biological":[73],"functions.":[74],"Other":[75],"algorithms":[76,248],"TreeDet":[79],"compute":[80],"classification":[82],"then":[84],"predict":[85,138],"associated":[88],"with":[89,246],"it.":[90],"However,":[91],"there":[92],"are":[93,213,281,297],"still":[94],"many":[95],"unresolved":[96],"questions:":[97],"Was":[98],"optimal":[100],"subdivision":[101],"family":[105],"achieved?":[106],"Do":[107],"definitions":[109],"at":[110,299],"different":[111],"levels":[112],"phylogenetic":[115,126,164],"tree":[116,127],"affect":[117],"prediction":[119],"positions?":[122,140],"Can":[123],"whole":[125,193],"be":[128],"used":[129,293],"instead":[130],"only":[132],"one":[133],"level":[134,168],"it":[136],"RESULTS:":[141],"Here":[142],"we":[143],"present":[144],"novel":[146,227],"method,":[147],"TEA-O":[148,187,223,244],"(Two-entropies":[149],"analysis-Objective),":[150],"trace":[152],"evolutionary":[154,183,269],"pressure":[155,270],"root":[158],"branches":[161],"tree.":[165],"At":[166],"each":[167],"tree,":[171],"TEA":[173],"plot":[174,188],"is":[175,189,262],"produced":[176],"capture":[178],"signal":[180],"pressure.":[184],"A":[185],"consensus":[186,285],"composed":[190],"series":[194],"plots":[196],"provide":[198],"condensed":[200],"representation.":[201],"Positions":[202],"related":[203],"functions":[205],"evolved":[207],"early":[208],"(conserved)":[209],"later":[211],"(specificity)":[212],"close":[214],"lower-left":[217],"upper-left":[219],"corner":[220],"plot,":[224],"respectively.":[225],"approach":[228],"an":[230],"unbiased,":[231],"user-independent,":[232],"residue":[235],"relevance":[236],"family.":[240],"We":[241],"compared":[242],"our":[243,260],"method":[245,261],"using":[249],"both":[250],"synthetic":[251],"real":[253],"sequences.":[255],"The":[256],"results":[257],"show":[258],"robust,":[263],"sensitive":[264],"subtle":[266],"during":[271],"evolution":[272],"comprehensive":[274],"because":[275],"all":[276],"MSA":[280],"presented":[282],"plot.":[286],"AVAILABILITY:":[287],"All":[288],"computer":[289],"programs":[290],"datasets":[292],"this":[295],"work":[296],"available":[298],"http://nava.liacs.nl/kye/TEA-O/":[300],"academic":[302],"use.":[303]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2016-06-24T00:00:00"}