{"id":"https://openalex.org/W2794847726","doi":"https://doi.org/10.1186/s12859-018-2074-9","title":"BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines","display_name":"BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines","publication_year":2018,"publication_date":"2018-03-02","ids":{"openalex":"https://openalex.org/W2794847726","doi":"https://doi.org/10.1186/s12859-018-2074-9","mag":"2794847726","pmid":"https://pubmed.ncbi.nlm.nih.gov/29499649"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2074-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2074-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2074-9.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2074-9.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077459482","display_name":"Y\u00f6zen Hern\u00e1ndez","orcid":"https://orcid.org/0000-0003-3349-8856"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Y\u00f6zen Hern\u00e1ndez","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","Graduate Program in Bioinformatics, Boston University, Boston, MA, 02215, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]},{"raw_affiliation_string":"Graduate Program in Bioinformatics, Boston University, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077472485","display_name":"Rocky Bernstein","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rocky Bernstein","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103431648","display_name":"Pedro E Pagan","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pedro Pagan","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033300014","display_name":"Levy C Vargas","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Levy Vargas","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085622837","display_name":"William D. McCaig","orcid":"https://orcid.org/0000-0002-3375-8710"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William McCaig","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021910428","display_name":"Girish Ramrattan","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Girish Ramrattan","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040340167","display_name":"Saymon Akther","orcid":"https://orcid.org/0000-0002-9084-9379"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saymon Akther","raw_affiliation_strings":["Graduate Center, City University of New York, New York, 10016, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Center, City University of New York, New York, 10016, USA","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I121847817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110192350","display_name":"Amanda M. Larracuente","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda Larracuente","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058344003","display_name":"Lia Di","orcid":"https://orcid.org/0000-0003-1957-6475"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lia Di","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089541949","display_name":"Filipe Garrett Vieira","orcid":"https://orcid.org/0000-0002-8464-7770"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I4210110903","display_name":"Natural History Museum Aarhus","ror":"https://ror.org/0166x0j30","country_code":"DK","type":"archive","lineage":["https://openalex.org/I4210110903"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Filipe G. Vieira","raw_affiliation_strings":["Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I4210110903","https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058885083","display_name":"Weigang Qiu","orcid":"https://orcid.org/0000-0003-4585-1872"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei-Gang Qiu","raw_affiliation_strings":["Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA. weigang@genectr.hunter.cuny.edu","Department of Physiology and Biophysics & Institute for Computational Biomedicine, Weil Cornell Medical College, New York, NY, 10021, USA. weigang@genectr.hunter.cuny.edu","Graduate Center, City University of New York, New York, 10016, USA. weigang@genectr.hunter.cuny.edu","Graduate Center, City University of New York, New York, 10016, USA"],"raw_orcid":"https://orcid.org/0000-0003-4585-1872","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Hunter College, City University of New York, New York, 10065, USA. weigang@genectr.hunter.cuny.edu","institution_ids":["https://openalex.org/I39694355"]},{"raw_affiliation_string":"Department of Physiology and Biophysics & Institute for Computational Biomedicine, Weil Cornell Medical College, New York, NY, 10021, USA. weigang@genectr.hunter.cuny.edu","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Graduate Center, City University of New York, New York, 10016, USA. weigang@genectr.hunter.cuny.edu","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I121847817","https://openalex.org/I174216632"]},{"raw_affiliation_string":"Graduate Center, City University of New York, New York, 10016, USA","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I121847817"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5058885083"],"corresponding_institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632","https://openalex.org/I205783295","https://openalex.org/I39694355"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0826,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.76499063,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"1","first_page":"76","last_page":"76"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8353999853134155,"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":0.8353999853134155,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.07000000029802322,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.03669999912381172,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.9334680438041687},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7970619201660156},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7550721168518066},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.6774404644966125},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5809130668640137},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.5799987316131592},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5552614331245422},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5270167589187622},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.5128514766693115},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4828963279724121},{"id":"https://openalex.org/keywords/codebase","display_name":"Codebase","score":0.47156092524528503},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.45760464668273926},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.29069626331329346},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10427680611610413}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.9334680438041687},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7970619201660156},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7550721168518066},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.6774404644966125},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5809130668640137},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.5799987316131592},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5552614331245422},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5270167589187622},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5128514766693115},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4828963279724121},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.47156092524528503},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.45760464668273926},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.29069626331329346},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10427680611610413}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-018-2074-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2074-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2074-9.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29499649","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29499649","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:academicworks.cuny.edu:hc_pubs-1408","is_oa":true,"landing_page_url":"https://academicworks.cuny.edu/hc_pubs/381","pdf_url":"https://academicworks.cuny.edu/hc_pubs/381","source":{"id":"https://openalex.org/S4377196304","display_name":"CUNY Academic Works (City University of New York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I174216632","host_organization_name":"City University of New York","host_organization_lineage":["https://openalex.org/I174216632"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Publications and Research","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/945bfa02-3b06-4aa5-8cb7-6a58de194ceb","is_oa":true,"landing_page_url":"https://curis.ku.dk/portal/da/publications/bpwrapper(945bfa02-3b06-4aa5-8cb7-6a58de194ceb).html","pdf_url":"https://curis.ku.dk/ws/files/195760220/BpWrapper_BioPerl_based_sequence_and_tree_utilities_for_rapid_prototyping_of_bioinformatics_pipelines.pdf","source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Hernandez , Y , Bernstein , R , Pagan , P , Vargas , L , McCaig , W , Ramrattan , G , Akther , S , Larracuente , A , Di , L , Vieira , F J G & Qiu , W-G 2018 , ' BpWrapper : BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines ' , B M C Bioinformatics , vol. 19 , 76 . https://doi.org/10.1186/s12859-018-2074-9","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/945bfa02-3b06-4aa5-8cb7-6a58de194ceb","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/945bfa02-3b06-4aa5-8cb7-6a58de194ceb","pdf_url":"https://researchprofiles.ku.dk/files/195760220/BpWrapper_BioPerl_based_sequence_and_tree_utilities_for_rapid_prototyping_of_bioinformatics_pipelines.pdf","source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Hernandez , Y , Bernstein , R , Pagan , P , Vargas , L , McCaig , W , Ramrattan , G , Akther , S , Larracuente , A , Di , L , Vieira , F J G & Qiu , W-G 2018 , ' BpWrapper : BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines ' , B M C Bioinformatics , vol. 19 , 76 . https://doi.org/10.1186/s12859-018-2074-9","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:0275901365564981b4ea66b2e6175b50","is_oa":true,"landing_page_url":"https://doaj.org/article/0275901365564981b4ea66b2e6175b50","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-7 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4746796","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5833151","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2074-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2074-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2074-9.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G1078746994","display_name":null,"funder_award_id":"MD007599","funder_id":"https://openalex.org/F4320337534","funder_display_name":"National Institute on Minority Health and Health Disparities"},{"id":"https://openalex.org/G2031133245","display_name":null,"funder_award_id":"AI107955","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2813607127","display_name":null,"funder_award_id":"T34 GM007823","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G385769981","display_name":null,"funder_award_id":"R21 AI139782","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3895041929","display_name":null,"funder_award_id":"G12 MD007599","funder_id":"https://openalex.org/F4320337534","funder_display_name":"National Institute on Minority Health and Health Disparities"},{"id":"https://openalex.org/G4049032510","display_name":null,"funder_award_id":"SC1 AI107955","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4071493736","display_name":null,"funder_award_id":"MD007599","funder_id":"https://openalex.org/F4320337374","funder_display_name":"National Center on Minority Health and Health Disparities"},{"id":"https://openalex.org/G420785507","display_name":null,"funder_award_id":"MD007599","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6289708505","display_name":null,"funder_award_id":"R25 GM060665","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8947429665","display_name":null,"funder_award_id":"MD007599","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337374","display_name":"National Center on Minority Health and Health Disparities","ror":"https://ror.org/0493hgw16"},{"id":"https://openalex.org/F4320337534","display_name":"National Institute on Minority Health and Health Disparities","ror":"https://ror.org/0493hgw16"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2794847726.pdf","grobid_xml":"https://content.openalex.org/works/W2794847726.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W26485700","https://openalex.org/W1526952949","https://openalex.org/W1996423252","https://openalex.org/W2031611770","https://openalex.org/W2043702114","https://openalex.org/W2114850508","https://openalex.org/W2132926880","https://openalex.org/W2141894068","https://openalex.org/W2150934173","https://openalex.org/W2157701114","https://openalex.org/W2346143774","https://openalex.org/W2588701839","https://openalex.org/W2924178771","https://openalex.org/W2982480066"],"related_works":["https://openalex.org/W2475789275","https://openalex.org/W2331989206","https://openalex.org/W3173828731","https://openalex.org/W2745097874","https://openalex.org/W2508823388","https://openalex.org/W45658120","https://openalex.org/W2225951319","https://openalex.org/W2008612003","https://openalex.org/W4405644016","https://openalex.org/W613088223"],"abstract_inverted_index":{"BACKGROUND:":[0],"Automated":[1],"bioinformatics":[2,29,119,312],"workflows":[3,299],"are":[4,157,166,288],"more":[5,12],"robust,":[6,72],"easier":[7],"to":[8,31,37,66,112,117,180,199],"maintain,":[9],"and":[10,73,137,149,163,201,209,259,275,286,310],"results":[11],"reproducible":[13],"when":[14],"built":[15],"with":[16,20,129],"command-line":[17,50,131,161,257,302],"utilities":[18,24,51,90,128,172,177,184,240,249,281],"than":[19],"custom-coded":[21],"scripts.":[22],"Command-line":[23],"further":[25],"benefit":[26],"by":[27,241],"relieving":[28],"developers":[30],"learn":[32],"the":[33,70,101,109,216,243,301],"use":[34],"of,":[35],"or":[36],"interact":[38],"directly":[39],"with,":[40],"biological":[41,57,76],"software":[42,58],"libraries.":[43],"There":[44],"is":[45,213,227],"however":[46],"a":[47,80,154,252],"lack":[48],"of":[49,69,83,98,100,124,142,170,175,182,246,267,272,298],"that":[52,174,181],"leverage":[53],"popular":[54,103],"Open":[55],"Source":[56,225],"toolkits":[59],"such":[60,250],"as":[61,88,114,116,160],"BioPerl":[62,104,193],"(":[63],"http://bioperl.org":[64],")":[65],"make":[67],"many":[68],"well-designed,":[71],"routinely":[74],"used":[75],"classes":[77],"available":[78,159,214,228],"for":[79,91,140,262,270,295,307],"wider":[81],"base":[82],"end":[84],"users.":[85],"RESULTS:":[86],"Designed":[87],"standard":[89,260],"UNIX-family":[92],"operating":[93,202],"systems,":[94],"BpWrapper":[95,125,171,188,235,293],"makes":[96],"functionality":[97],"some":[99],"most":[102],"modules":[105],"readily":[106],"accessible":[107],"on":[108,186,192,229,237,300],"command":[110],"line":[111],"novice":[113],"well":[115],"experienced":[118],"practitioners.":[120],"The":[121],"initial":[122],"release":[123],"includes":[126],"four":[127],"concise":[130,253],"user":[132,254],"interfaces,":[133],"bioseq,":[134],"bioaln,":[135],"biotree,":[136],"biopop,":[138],"specialized":[139],"manipulation":[141,271],"molecular":[143],"sequences,":[144,273],"sequence":[145,239],"alignments,":[146,274],"phylogenetic":[147,276],"trees,":[148,277],"DNA":[150],"polymorphisms,":[151],"respectively.":[152],"Over":[153],"hundred":[155],"methods":[156,165,269],"currently":[158],"options":[162],"new":[164],"easily":[167],"incorporated.":[168],"Performance":[169],"lags":[173],"precompiled":[176],"while":[178],"equivalent":[179],"other":[183,311],"based":[185],"BioPerl.":[187],"has":[189],"been":[190],"tested":[191],"Release":[194,211],"1.6,":[195],"Perl":[196,218],"versions":[197],"5.10.1":[198],"5.25.10,":[200],"systems":[203],"including":[204,251],"Apple":[205],"macOS,":[206],"Microsoft":[207],"Windows,":[208],"GNU/Linux.":[210],"code":[212,226],"from":[215],"Comprehensive":[217],"Archive":[219],"Network":[220],"(CPAN)":[221],"at":[222,231],"https://metacpan.org/pod/Bio::BPWrapper":[223],".":[224,233],"GitHub":[230],"https://github.com/bioperl/p5-bpwrapper":[232],"CONCLUSIONS:":[234],"improves":[236],"existing":[238,280],"following":[242],"design":[244],"principles":[245],"Unix":[247],"text":[248],"interface,":[255],"extensive":[256],"options,":[258],"input/output":[261],"serialized":[263],"operations.":[264],"Further,":[265],"dozens":[266],"novel":[268],"unavailable":[278],"in":[279],"(e.g.,":[282],"EMBOSS,":[283],"Newick":[284],"Utilities,":[285],"FAST),":[287],"provided.":[289],"Bioinformaticians":[290],"should":[291],"find":[292],"useful":[294],"rapid":[296],"prototyping":[297],"without":[303],"creating":[304],"custom":[305],"scripts":[306],"comparative":[308],"genomics":[309],"applications.":[313]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}