{"id":"https://openalex.org/W2119801041","doi":"https://doi.org/10.1093/nar/gkp373","title":"Berkeley PHOG: PhyloFacts orthology group prediction web server","display_name":"Berkeley PHOG: PhyloFacts orthology group prediction web server","publication_year":2009,"publication_date":"2009-05-12","ids":{"openalex":"https://openalex.org/W2119801041","doi":"https://doi.org/10.1093/nar/gkp373","mag":"2119801041","pmid":"https://pubmed.ncbi.nlm.nih.gov/19435885"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkp373","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp373","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W84/16758453/gkp373.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W84/16758453/gkp373.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034710937","display_name":"Ruchira S. Datta","orcid":"https://orcid.org/0000-0003-2130-5818"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruchira S. Datta","raw_affiliation_strings":["QB3 Institute, University of California, Berkeley, CA, USA. ruchira@berkeley.edu","QB3 Institute, University of California, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, University of California, Berkeley, CA, USA. ruchira@berkeley.edu","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]},{"raw_affiliation_string":"QB3 Institute, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000439104","display_name":"Christopher A. Meacham","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Meacham","raw_affiliation_strings":["QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I103922791"]},{"raw_affiliation_string":"QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036130616","display_name":"Bushra Samad","orcid":"https://orcid.org/0000-0002-2893-0897"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bushra Samad","raw_affiliation_strings":["QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I103922791"]},{"raw_affiliation_string":"QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051244205","display_name":"Christoph Neyer","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christoph Neyer","raw_affiliation_strings":["QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I103922791"]},{"raw_affiliation_string":"QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107849607","display_name":"Kimmen Sj\u00f6lander","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kimmen Sj\u00f6lander","raw_affiliation_strings":["QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I103922791"]},{"raw_affiliation_string":"QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5034710937"],"corresponding_institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.5336,"has_fulltext":false,"cited_by_count":73,"citation_normalized_percentile":{"value":0.95664064,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"suppl_2","first_page":"W84","last_page":"W89"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9545999765396118,"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":0.9545999765396118,"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/T10885","display_name":"Gene expression and cancer classification","score":0.942300021648407,"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/biology","display_name":"Biology","score":0.9579502940177917},{"id":"https://openalex.org/keywords/group","display_name":"Group (periodic table)","score":0.6020894646644592},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5226821303367615},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38178303837776184},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3806562125682831},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2723228335380554},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.10072764754295349}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9579502940177917},{"id":"https://openalex.org/C2781311116","wikidata":"https://www.wikidata.org/wiki/Q83306","display_name":"Group (periodic table)","level":2,"score":0.6020894646644592},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5226821303367615},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38178303837776184},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3806562125682831},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2723228335380554},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.10072764754295349},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000818","descriptor_name":"Animals","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":"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":"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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkp373","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp373","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W84/16758453/gkp373.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:19435885","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19435885","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.521.3583","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.521.3583","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/37/suppl_2/W84.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.629.3699","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.629.3699","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/early/2009/05/12/nar.gkp373.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.632.2639","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.632.2639","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/early/2009/05/12/nar.gkp373.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.788.1095","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.788.1095","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/24/e2/gkp373.PMC2703887.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2703887","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2703887","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkp373","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp373","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W84/16758453/gkp373.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7867243371","display_name":null,"funder_award_id":"R01HG02769","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W319819633","https://openalex.org/W1958476169","https://openalex.org/W1974160388","https://openalex.org/W1977027195","https://openalex.org/W2027542060","https://openalex.org/W2028265997","https://openalex.org/W2029833898","https://openalex.org/W2055033601","https://openalex.org/W2056568233","https://openalex.org/W2057885377","https://openalex.org/W2094290815","https://openalex.org/W2104558151","https://openalex.org/W2107251251","https://openalex.org/W2119027485","https://openalex.org/W2120864016","https://openalex.org/W2124410686","https://openalex.org/W2124815061","https://openalex.org/W2154364831","https://openalex.org/W2155606054","https://openalex.org/W2159266221","https://openalex.org/W2166705366","https://openalex.org/W2167188257","https://openalex.org/W2167455933","https://openalex.org/W4210580032","https://openalex.org/W4252706339"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191","https://openalex.org/W2117258802"],"abstract_inverted_index":{"Ortholog":[0],"detection":[1],"is":[2,142,180],"essential":[3],"in":[4,147],"functional":[5],"annotation":[6],"of":[7,16,59,84,161],"genomes,":[8],"with":[9,65,158],"applications":[10],"to":[11,34,73,168],"phylogenetic":[12,39],"tree":[13],"construction,":[14],"prediction":[15],"protein-protein":[17],"interaction":[18],"and":[19,62,68,70,78,93,151,173],"other":[20],"bioinformatics":[21],"tasks.":[22],"We":[23],"present":[24],"here":[25],"the":[26,47,82,148],"PHOG":[27,55,105,123,141,177],"web":[28,178],"server":[29,179],"employing":[30],"a":[31,43,57,100,122,159],"novel":[32],"algorithm":[33],"identify":[35],"orthologs":[36,165],"based":[37,143],"on":[38,42,96,118,144],"analysis.":[40],"Results":[41],"benchmark":[44],"dataset":[45],"from":[46],"TreeFam-A":[48],"manually":[49],"curated":[50],"orthology":[51,156],"database":[52],"show":[53],"that":[54],"provides":[56],"combination":[58],"high":[60,127],"recall":[61,92,109,114,128,131],"precision":[63,79,95,103,117,136],"competitive":[64],"both":[66],"InParanoid":[67,111],"OrthoMCL,":[69],"allows":[71],"users":[72],"target":[74],"different":[75],"taxonomic":[76],"distances":[77],"levels":[80],"through":[81],"use":[83],"tree-distance":[85],"thresholds.":[86],"For":[87],"instance,":[88],"OrthoMCL-DB":[89],"achieved":[90,112],"76%":[91],"66%":[94],"this":[97,119],"dataset;":[98],"at":[99,115,132,182],"slightly":[101],"higher":[102,108],"(68%)":[104],"achieves":[106,129],"10%":[107],"(86%).":[110],"87%":[113],"24%":[116],"dataset,":[120],"while":[121],"variant":[124],"designed":[125],"for":[126],"88%":[130],"61%":[133],"precision,":[134],"increasing":[135],"by":[137],"37%":[138],"over":[139,153],"InParanoid.":[140],"pre-computed":[145],"trees":[146],"PhyloFacts":[149],"resource,":[150],"contains":[152],"366":[154],"K":[155],"groups":[157],"minimum":[160],"three":[162],"species.":[163],"Predicted":[164],"are":[166],"linked":[167],"GO":[169],"annotations,":[170],"pathway":[171],"information":[172],"biological":[174],"literature.":[175],"The":[176],"available":[181],"http://phylofacts.berkeley.edu/orthologs/.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":12}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}