{"id":"https://openalex.org/W2125904165","doi":"https://doi.org/10.1093/bioinformatics/btu645","title":"DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML","display_name":"DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML","publication_year":2014,"publication_date":"2014-10-07","ids":{"openalex":"https://openalex.org/W2125904165","doi":"https://doi.org/10.1093/bioinformatics/btu645","mag":"2125904165","pmid":"https://pubmed.ncbi.nlm.nih.gov/25294920"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/416/17126231/btu645.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/416/17126231/btu645.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052424104","display_name":"Ryan M. Ames","orcid":"https://orcid.org/0000-0002-1432-5629"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Ryan M. Ames","raw_affiliation_strings":["Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000605194","display_name":"Simon C. Lovell","orcid":"https://orcid.org/0000-0002-4092-8458"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Simon C. Lovell","raw_affiliation_strings":["Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5052424104"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.11482117,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"31","issue":"3","first_page":"416","last_page":"417"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3418999910354614,"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":0.3418999910354614,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.24469999969005585,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.10769999772310257,"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/computer-science","display_name":"Computer science","score":0.6949796676635742},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6145015358924866},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5668576955795288},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4661981165409088},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.32777589559555054}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6949796676635742},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6145015358924866},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5668576955795288},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4661981165409088},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.32777589559555054}],"mesh":[{"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":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":"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":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btu645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/416/17126231/btu645.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25294920","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25294920","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:3302187","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4308661","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:oai:pure.atira.dk:openaire_cris_publications/7413d3ac-f3ea-43f5-ba07-78ed16632271","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/7413d3ac-f3ea-43f5-ba07-78ed16632271","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ames, R M & Lovell, S C 2015, 'DupliPHY-Web: A web server for DupliPHY and DupliPHY-ML', Bioinformatics, vol. 31, no. 3, pp. 416-7. https://doi.org/10.1093/bioinformatics/btu645","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.atira.dk:publications/7413d3ac-f3ea-43f5-ba07-78ed16632271","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/dupliphyweb-a-web-server-for-dupliphy-and-dupliphyml(7413d3ac-f3ea-43f5-ba07-78ed16632271).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ames, R M & Lovell, S C 2015, 'DupliPHY-Web: A web server for DupliPHY and DupliPHY-ML', Bioinformatics, vol. 31, no. 3, pp. 416-7. https://doi.org/10.1093/bioinformatics/btu645","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/3/416/17126231/btu645.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2888716957","display_name":null,"funder_award_id":"BB/I020489/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5052588576","display_name":"Understanding the Retention of Genes Following Duplication","funder_award_id":"BB/I020489/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125904165.pdf","grobid_xml":"https://content.openalex.org/works/W2125904165.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1641544182","https://openalex.org/W2011889195","https://openalex.org/W2019591778","https://openalex.org/W2081933515","https://openalex.org/W2095829109","https://openalex.org/W2106013076","https://openalex.org/W2114430361","https://openalex.org/W2115300733","https://openalex.org/W2129106405","https://openalex.org/W2135123683","https://openalex.org/W4229487902"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"SUMMARY:":[0],"Gene":[1],"duplication":[2,19],"and":[3,20,67,85],"loss":[4],"are":[5,109],"important":[6,24,44],"processes":[7],"in":[8,46],"the":[9,33,37,48],"evolution":[10,49],"of":[11,16,40,50],"gene":[12,62],"families.":[13],"Moreover,":[14],"growth":[15],"families":[17,41],"by":[18,26],"retention":[21],"is":[22,42,98],"an":[23,43,88],"mechanism":[25],"which":[27],"organisms":[28],"gain":[29],"new":[30],"functions.":[31],"Therefore":[32],"ability":[34],"to":[35,60,91],"infer":[36,61],"evolutionary":[38],"histories":[39,64],"step":[45],"understanding":[47],"function.":[51],"We":[52],"have":[53],"recently":[54],"developed":[55],"DupliPHY,":[56],"a":[57,74],"software":[58],"tool":[59],"family":[63],"using":[65],"parsimony":[66],"maximum":[68,82],"likelihood.":[69],"Here,":[70],"we":[71],"present":[72],"DupliPHY-Web":[73,97],"web":[75],"server":[76],"for":[77],"DupliPHY":[78],"that":[79],"implements":[80],"additional":[81],"likelihood":[83],"functionality":[84],"provides":[86],"users":[87],"intuitive":[89],"interface":[90],"run":[92],"DupliPHY.":[93],"AVAILABILITY":[94],"AND":[95],"IMPLEMENTATION:":[96],"available":[99,110],"at":[100,111],"www.bioinf.manchester.ac.uk/dupliphy/":[101],"CONTACT:":[102],":":[103],"ryan.ames@manchester.ac.uk":[104],"SUPPLEMENTARY":[105],"INFORMATION:":[106],"Supplementary":[107],"data":[108],"Bioinformatics":[112],"online.":[113]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}