{"id":"https://openalex.org/W2046951963","doi":"https://doi.org/10.1093/nar/gkt399","title":"The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification","display_name":"The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification","publication_year":2013,"publication_date":"2013-05-18","ids":{"openalex":"https://openalex.org/W2046951963","doi":"https://doi.org/10.1093/nar/gkt399","mag":"2046951963","pmid":"https://pubmed.ncbi.nlm.nih.gov/23685612"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt399","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W242/16942581/gkt399.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","license_id":"https://openalex.org/licenses/cc-by","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/41/W1/W242/16942581/gkt399.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063582056","display_name":"Cyrus Afrasiabi","orcid":null},"institutions":[{"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":"Cyrus Afrasiabi","raw_affiliation_strings":["QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA","1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, 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/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, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006434469","display_name":"David Dineen","orcid":null},"institutions":[{"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":"David Dineen","raw_affiliation_strings":["QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["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/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, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, 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/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":"Kimmen Sj\u00f6lander","raw_affiliation_strings":["QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2 Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA and 2Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720-1762, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5107849607"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.9264,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.85716772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"41","issue":"W1","first_page":"W242","last_page":"W248"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9987000226974487,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9567000269889832,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9549999833106995,"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/biology","display_name":"Biology","score":0.7683740854263306},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.7030682563781738},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.6143878698348999},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6021047830581665},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5829154253005981},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5388161540031433},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49948596954345703},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49384957551956177},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.4701923131942749},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.4701160490512848},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.461703360080719},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4510393440723419},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.44141528010368347},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39449000358581543},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3227229416370392},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26758962869644165},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19586235284805298},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18360745906829834},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.12018725275993347},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09897032380104065},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.08553794026374817}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7683740854263306},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.7030682563781738},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.6143878698348999},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6021047830581665},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5829154253005981},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5388161540031433},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49948596954345703},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49384957551956177},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4701923131942749},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.4701160490512848},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.461703360080719},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4510393440723419},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.44141528010368347},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39449000358581543},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3227229416370392},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26758962869644165},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19586235284805298},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18360745906829834},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.12018725275993347},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09897032380104065},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.08553794026374817},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0}],"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":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkt399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt399","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W242/16942581/gkt399.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:23685612","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23685612","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:osti.gov:1904526","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1904526","pdf_url":"https://www.osti.gov/servlets/purl/1904526","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org/ark:/13030/qt3vd3s7dr","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/3vd3s7dr","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol 41, iss W1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2686063","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3692063","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:qt3vd3s7dr","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/3vd3s7dr","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Afrasiabi, C.; Samad, B.; Dineen, D.; Meacham, C.; & Sjolander, K.(2013). The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. Nucleic Acids Research, 41(W1), W242 - W248. doi: 10.1093/nar/gkt399. UC Berkeley: UC Berkeley Library. Retrieved from: http://www.escholarship.org/uc/item/3vd3s7dr","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkt399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt399","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W242/16942581/gkt399.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2046951963.pdf","grobid_xml":"https://content.openalex.org/works/W2046951963.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1958476169","https://openalex.org/W1974160388","https://openalex.org/W1977027195","https://openalex.org/W1998767819","https://openalex.org/W2024812560","https://openalex.org/W2027542060","https://openalex.org/W2031611770","https://openalex.org/W2038184529","https://openalex.org/W2048448217","https://openalex.org/W2082202339","https://openalex.org/W2097485877","https://openalex.org/W2112162865","https://openalex.org/W2119801041","https://openalex.org/W2121013757","https://openalex.org/W2141885858","https://openalex.org/W2143335572","https://openalex.org/W2146709375","https://openalex.org/W2166705366","https://openalex.org/W2167347821","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W2380915035","https://openalex.org/W2298047311","https://openalex.org/W4242909373","https://openalex.org/W2361861616","https://openalex.org/W1997697005","https://openalex.org/W2308248996","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2105364679"],"abstract_inverted_index":{"The":[0,75,171],"PhyloFacts":[1,31,148],"'Fast":[2],"Approximate":[3],"Tree":[4,108],"Classification'":[5],"(FAT-CAT)":[6],"web":[7,173],"server":[8,174],"provides":[9],"a":[10,35,83],"novel":[11],"approach":[12],"to":[13,25,55,81,113,129,167],"ortholog":[14,66],"identification":[15,67],"using":[16,158],"subtree":[17,70],"hidden":[18,71],"Markov":[19,72],"model-based":[20],"placement":[21,78],"of":[22,38,65,109],"protein":[23],"sequences":[24,136],"phylogenomic":[26],"orthology":[27],"groups":[28],"in":[29],"the":[30,63,87,107,151,159],"database.":[32],"Results":[33],"on":[34,69],"data":[36],"set":[37],"microbial,":[39],"plant":[40],"and":[41,51,53,92,98,116,137,164],"animal":[42],"proteins":[43,104,138],"demonstrate":[44],"FAT-CAT's":[45],"high":[46],"precision":[47,64],"at":[48,177],"separating":[49],"orthologs":[50,115],"paralogs":[52],"robustness":[54],"promiscuous":[56,140],"domains.":[57],"We":[58],"also":[59,144],"present":[60],"results":[61],"documenting":[62],"based":[68],"model":[73],"scoring.":[74],"FAT-CAT":[76,112,172],"phylogenetic":[77],"is":[79,175],"used":[80],"derive":[82],"functional":[84,99],"annotation":[85],"for":[86,119],"query,":[88],"including":[89,134],"confidence":[90],"scores":[91],"drill-down":[93],"capabilities.":[94],"PhyloFacts'":[95],"broad":[96],"taxonomic":[97],"coverage,":[100],"with":[101],">7.3":[102],"M":[103],"from":[105],"across":[106],"Life,":[110],"enables":[111],"predict":[114],"assign":[117],"function":[118],"most":[120],"sequence":[121,132],"inputs.":[122],"Four":[123],"pipeline":[124],"parameter":[125],"presets":[126],"are":[127,165],"provided":[128],"handle":[130],"different":[131],"types,":[133],"partial":[135],"containing":[139],"domains;":[141],"users":[142],"can":[143,153],"modify":[145],"individual":[146],"parameters.":[147],"trees":[149],"matching":[150],"query":[152],"be":[154],"viewed":[155],"interactively":[156],"online":[157],"PhyloScope":[160],"Javascript":[161],"tree":[162],"viewer":[163],"hyperlinked":[166],"various":[168],"external":[169],"databases.":[170],"available":[176],"http://phylogenomics.berkeley.edu/phylofacts/fatcat/.":[178]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}