{"id":"https://openalex.org/W2203551296","doi":"https://doi.org/10.1093/bioinformatics/btw051","title":"S<scp>weep</scp>F<scp>inder</scp>2: increased sensitivity, robustness and flexibility","display_name":"S<scp>weep</scp>F<scp>inder</scp>2: increased sensitivity, robustness and flexibility","publication_year":2016,"publication_date":"2016-02-15","ids":{"openalex":"https://openalex.org/W2203551296","doi":"https://doi.org/10.1093/bioinformatics/btw051","mag":"2203551296","pmid":"https://pubmed.ncbi.nlm.nih.gov/27153702"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw051","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/1895/6688148/btw051.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/32/12/1895/6688148/btw051.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107393193","display_name":"Michael DeGiorgio","orcid":null},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael DeGiorgio","raw_affiliation_strings":["1 Department of Biology and Institute for CyberScience, Pennsylvania State University, University Park, PA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biology and Institute for CyberScience, Pennsylvania State University, University Park, PA, USA,","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019533423","display_name":"Christian D. Huber","orcid":"https://orcid.org/0000-0002-2267-2604"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christian D. Huber","raw_affiliation_strings":["2 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA,","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076289653","display_name":"Melissa J. Hubisz","orcid":"https://orcid.org/0000-0002-9561-6830"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa J. Hubisz","raw_affiliation_strings":["3 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA,","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068212916","display_name":"Ines Hellmann","orcid":"https://orcid.org/0000-0003-0588-1313"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ines Hellmann","raw_affiliation_strings":["4 Department Biologie II, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Planegg-Martinsried, Germany and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Department Biologie II, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Planegg-Martinsried, Germany and","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088476239","display_name":"Rasmus Nielsen","orcid":"https://orcid.org/0000-0003-0513-6591"},"institutions":[{"id":"https://openalex.org/I4210100046","display_name":"Integra (United States)","ror":"https://ror.org/00ynqbp15","country_code":"US","type":"company","lineage":["https://openalex.org/I4210100046"]},{"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":"Rasmus Nielsen","raw_affiliation_strings":["5 Department of Integrative Biology, University of California, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5 Department of Integrative Biology, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I4210100046","https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5107393193"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":38.1056,"has_fulltext":false,"cited_by_count":382,"citation_normalized_percentile":{"value":0.99792046,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"32","issue":"12","first_page":"1895","last_page":"1897"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.2973000109195709,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.2973000109195709,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.09600000083446503,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.06620000302791595,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/robustness","display_name":"Robustness (evolution)","score":0.8046993017196655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6176891922950745},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.48873281478881836},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22019225358963013},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2185499668121338},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16270849108695984},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06756770610809326}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.8046993017196655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6176891922950745},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48873281478881836},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22019225358963013},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2185499668121338},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16270849108695984},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06756770610809326}],"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":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","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":"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":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":false},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw051","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/1895/6688148/btw051.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:27153702","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27153702","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:escholarship.org:ark:/13030/qt3726f8t5","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/3726f8t5","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 32, iss 12","raw_type":"article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/12/1895","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/12/1895","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw051","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/12/1895/6688148/btw051.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1815908729","https://openalex.org/W1900103465","https://openalex.org/W1900500601","https://openalex.org/W1925508000","https://openalex.org/W1989923963","https://openalex.org/W1997898977","https://openalex.org/W2009132217","https://openalex.org/W2010131461","https://openalex.org/W2013786537","https://openalex.org/W2025293107","https://openalex.org/W2032311106","https://openalex.org/W2050318259","https://openalex.org/W2059201551","https://openalex.org/W2103656106","https://openalex.org/W2103677370","https://openalex.org/W2109183238","https://openalex.org/W2109195195","https://openalex.org/W2111699978","https://openalex.org/W2126204254","https://openalex.org/W2136557734","https://openalex.org/W2141035297","https://openalex.org/W2141179727","https://openalex.org/W2149238797","https://openalex.org/W2155670634","https://openalex.org/W2156658072","https://openalex.org/W2161510059","https://openalex.org/W2163441392","https://openalex.org/W2166394292","https://openalex.org/W2167852412","https://openalex.org/W2168912878","https://openalex.org/W4251304755"],"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/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"UNLABELLED:":[0],"SweepFinder":[1,28],"is":[2,73,80],"a":[3,9,66,74,89],"widely":[4],"used":[5],"program":[6],"that":[7,50,79],"implements":[8],"powerful":[10],"likelihood-based":[11],"method":[12],"for":[13],"detecting":[14],"recent":[15],"positive":[16],"selection,":[17],"or":[18],"selective":[19],"sweeps.":[20],"Here,":[21],"we":[22],"present":[23],"SweepFinder2,":[24],"an":[25],"extension":[26],"of":[27,38],"with":[29],"increased":[30,48],"sensitivity":[31],"and":[32,42,64,84],"robustness":[33],"to":[34,54],"the":[35,52,59],"confounding":[36],"effects":[37],"mutation":[39],"rate":[40],"variation":[41],"background":[43],"selection.":[44],"Moreover,":[45],"SweepFinder2":[46,72],"has":[47],"flexibility":[49],"enables":[51],"user":[53],"specify":[55],"test":[56,62],"sites,":[57],"set":[58],"distance":[60],"between":[61],"sites":[63],"utilize":[65],"recombination":[67],"map.":[68],"AVAILABILITY":[69],"AND":[70],"IMPLEMENTATION:":[71],"freely-available":[75],"(www.personal.psu.edu/mxd60/sf2.html)":[76],"software":[77],"package":[78],"written":[81],"in":[82],"C":[83],"can":[85],"be":[86],"run":[87],"from":[88],"Unix":[90],"command":[91],"line.":[92],"CONTACT:":[93],"mxd60@psu.edu.":[94]},"counts_by_year":[{"year":2026,"cited_by_count":25},{"year":2025,"cited_by_count":49},{"year":2024,"cited_by_count":48},{"year":2023,"cited_by_count":36},{"year":2022,"cited_by_count":45},{"year":2021,"cited_by_count":76},{"year":2020,"cited_by_count":44},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":23},{"year":2017,"cited_by_count":11},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-10T07:06:39.071514","created_date":"2016-06-24T00:00:00"}
