{"id":"https://openalex.org/W2951890991","doi":"https://doi.org/10.1093/bioinformatics/btv646","title":"PHYLUCE is a software package for the analysis of conserved genomic loci","display_name":"PHYLUCE is a software package for the analysis of conserved genomic loci","publication_year":2015,"publication_date":"2015-11-02","ids":{"openalex":"https://openalex.org/W2951890991","doi":"https://doi.org/10.1093/bioinformatics/btv646","mag":"2951890991","pmid":"https://pubmed.ncbi.nlm.nih.gov/26530724"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv646","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv646","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/786/25588875/btv646.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/32/5/786/25588875/btv646.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038245887","display_name":"Brant C. Faircloth","orcid":"https://orcid.org/0000-0002-1943-0217"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]},{"id":"https://openalex.org/I1337608970","display_name":"Houston Museum of Natural Science","ror":"https://ror.org/02vtdx988","country_code":"US","type":"archive","lineage":["https://openalex.org/I1337608970"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brant C. Faircloth","raw_affiliation_strings":["Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA","institution_ids":["https://openalex.org/I121820613","https://openalex.org/I1337608970"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5038245887"],"corresponding_institution_ids":["https://openalex.org/I121820613","https://openalex.org/I1337608970"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":18.1928,"has_fulltext":false,"cited_by_count":1069,"citation_normalized_percentile":{"value":0.99572921,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"32","issue":"5","first_page":"786","last_page":"788"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.48899999260902405,"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":0.48899999260902405,"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/T10012","display_name":"Genetic diversity and population structure","score":0.29760000109672546,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.03460000082850456,"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/python","display_name":"Python (programming language)","score":0.796049952507019},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6707384586334229},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6187545657157898},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6020256876945496},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.5635196566581726},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.547605574131012},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.534991443157196},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.4955073595046997},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4900926351547241},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4851680397987366},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.41535499691963196},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3996224105358124},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3408328592777252},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2500113546848297},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15189126133918762},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09876501560211182}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.796049952507019},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6707384586334229},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6187545657157898},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6020256876945496},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.5635196566581726},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.547605574131012},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.534991443157196},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.4955073595046997},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4900926351547241},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4851680397987366},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.41535499691963196},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3996224105358124},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3408328592777252},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2500113546848297},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15189126133918762},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09876501560211182},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv646","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv646","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/786/25588875/btv646.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:26530724","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26530724","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:open-archive.highwire.org:bioinfo:32/5/786","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/5/786","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"},{"id":"pmh:oai:repository.lsu.edu:biosci_pubs-4716","is_oa":false,"landing_page_url":"https://repository.lsu.edu/biosci_pubs/3711","pdf_url":null,"source":{"id":"https://openalex.org/S4210169993","display_name":"Civil War Book Review","issn_l":"1528-6592","issn":["1528-6592"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310315936","host_organization_name":"Louisiana State University","host_organization_lineage":["https://openalex.org/P4310315936"],"host_organization_lineage_names":["Louisiana State University"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv646","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv646","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/786/25588875/btv646.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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1519266993","https://openalex.org/W1786896381","https://openalex.org/W1963580691","https://openalex.org/W1963957860","https://openalex.org/W1966822396","https://openalex.org/W2099111652","https://openalex.org/W2103088017","https://openalex.org/W2122302865","https://openalex.org/W2123639897","https://openalex.org/W2126419817","https://openalex.org/W2130526187","https://openalex.org/W2131271579","https://openalex.org/W2133870991","https://openalex.org/W2134285566","https://openalex.org/W2141052558","https://openalex.org/W2146058063","https://openalex.org/W2159957100","https://openalex.org/W2160378127","https://openalex.org/W2160969485","https://openalex.org/W2161444534","https://openalex.org/W2994240441","https://openalex.org/W3105939366","https://openalex.org/W6638274289","https://openalex.org/W6675475285","https://openalex.org/W6679658905"],"related_works":["https://openalex.org/W4292228088","https://openalex.org/W4309247532","https://openalex.org/W2137111266","https://openalex.org/W4323353411","https://openalex.org/W4220668561","https://openalex.org/W3096946169","https://openalex.org/W2113128227","https://openalex.org/W2144610372","https://openalex.org/W2119924680","https://openalex.org/W2098339479"],"abstract_inverted_index":{"UNLABELLED:":[0],"Targeted":[1],"enrichment":[2,39],"of":[3,12,17,37,92,96],"conserved":[4,63],"and":[5,68,70,82,94,113,146,161,168],"ultraconserved":[6],"genomic":[7],"elements":[8],"allows":[9],"universal":[10],"collection":[11],"phylogenomic":[13,76],"data":[14,33,170,181],"from":[15,34,47,54,127,166,173],"hundreds":[16,91],"species":[18],"at":[19,184],"multiple":[20],"time":[21],"scales":[22],"(<5":[23],"Ma":[24],"to":[25,30,44,65],">":[26],"300":[27],"Ma).":[28],"Prior":[29],"downstream":[31],"inference,":[32],"these":[35,72,88],"types":[36],"targeted":[38],"studies":[40],"must":[41],"undergo":[42],"preprocessing":[43],"assemble":[45],"contigs":[46,61],"sequence":[48],"data;":[49,58],"identify":[50],"targeted,":[51],"enriched":[52,60,97],"loci":[53,64],"the":[55,138],"off-target":[56],"background":[57],"align":[59],"representing":[62],"one":[66],"another;":[67],"prepare":[69],"manipulate":[71],"alignments":[73],"for":[74,105,137],"subsequent":[75],"inference.":[77],"PHYLUCE":[78,102,108,118,129,151],"is":[79,103,109,121,130],"an":[80],"efficient":[81],"easy-to-install":[83],"software":[84,159],"package":[85,135],"that":[86,142],"accomplishes":[87],"tasks":[89],"across":[90],"taxa":[93],"thousands":[95],"loci.":[98],"AVAILABILITY":[99],"AND":[100],"IMPLEMENTATION:":[101],"written":[104],"Python":[106,140],"2.7.":[107],"supported":[110],"on":[111,153],"OSX":[112],"Linux":[114],"(RedHat/CentOS)":[115],"operating":[116],"systems.":[117],"source":[119],"code":[120],"distributed":[122],"under":[123],"a":[124,134,150,162],"BSD-style":[125],"license":[126],"https://www.github.com/faircloth-lab/phyluce/":[128],"also":[131],"available":[132,165,172,183],"as":[133],"(https://binstar.org/faircloth-lab/phyluce)":[136],"Anaconda":[139],"distribution":[141],"installs":[143],"all":[144],"dependencies,":[145],"users":[147],"can":[148],"request":[149],"instance":[152],"iPlant":[154],"Atmosphere":[155],"(tag:":[156],"phyluce).":[157],"The":[158],"manual":[160],"tutorial":[163],"are":[164,171,182],"http://phyluce.readthedocs.org/en/latest/":[167],"test":[169],"doi:":[174],"10.6084/m9.figshare.1284521.":[175],"CONTACT:":[176],"brant@faircloth-lab.org":[177],"SUPPLEMENTARY":[178],"INFORMATION:":[179],"Supplementary":[180],"Bioinformatics":[185],"online.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":95},{"year":2025,"cited_by_count":158},{"year":2024,"cited_by_count":149},{"year":2023,"cited_by_count":114},{"year":2022,"cited_by_count":116},{"year":2021,"cited_by_count":134},{"year":2020,"cited_by_count":105},{"year":2019,"cited_by_count":66},{"year":2018,"cited_by_count":61},{"year":2017,"cited_by_count":42},{"year":2016,"cited_by_count":25},{"year":2015,"cited_by_count":4}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}