{"id":"https://openalex.org/W2128140984","doi":"https://doi.org/10.1186/1471-2105-9-175","title":"A perl package and an alignment tool for phylogenetic networks","display_name":"A perl package and an alignment tool for phylogenetic networks","publication_year":2008,"publication_date":"2008-03-27","ids":{"openalex":"https://openalex.org/W2128140984","doi":"https://doi.org/10.1186/1471-2105-9-175","mag":"2128140984","pmid":"https://pubmed.ncbi.nlm.nih.gov/18371228"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-175","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-175","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-175","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/counter/pdf/10.1186/1471-2105-9-175","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006561727","display_name":"Gabriel Cardona","orcid":"https://orcid.org/0000-0001-8845-4290"},"institutions":[{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gabriel Cardona","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma de Mallorca, Spain. gabriel.cardona@uib.es","Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma de Mallorca, Spain. gabriel.cardona@uib.es","institution_ids":["https://openalex.org/I50441567"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087466847","display_name":"Francesc Rossell\u00f3","orcid":"https://orcid.org/0000-0003-2897-5398"},"institutions":[{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francesc Rossell\u00f3","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122, Palma de Mallorca, Spain","Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122, Palma de Mallorca, Spain","institution_ids":["https://openalex.org/I50441567"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca (Spain)","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005629452","display_name":"Gabriel Valiente","orcid":"https://orcid.org/0000-0001-9194-2703"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Gabriel Valiente","raw_affiliation_strings":["Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain","Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006561727"],"corresponding_institution_ids":["https://openalex.org/I50441567"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3786,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.80531698,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"9","issue":"1","first_page":"175","last_page":"175"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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":0.9977999925613403,"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":0.9776999950408936,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9746000170707703,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.9749668836593628},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8374943733215332},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.7339810132980347},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.560626208782196},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4982433319091797},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4776407778263092},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.44507724046707153},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42264798283576965},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24778792262077332},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10288435220718384},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0842454731464386}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.9749668836593628},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8374943733215332},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.7339810132980347},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.560626208782196},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4982433319091797},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4776407778263092},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.44507724046707153},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42264798283576965},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24778792262077332},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10288435220718384},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0842454731464386}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-175","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-175","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-175","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:18371228","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18371228","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:doaj.org/article:e2a41064b5744c0a9c2a1326ae180ecb","is_oa":true,"landing_page_url":"https://doaj.org/article/e2a41064b5744c0a9c2a1326ae180ecb","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 175 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2330044","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2330044","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-175","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-175","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-175","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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128140984.pdf","grobid_xml":"https://content.openalex.org/works/W2128140984.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1996387066","https://openalex.org/W2060425093","https://openalex.org/W2096967818","https://openalex.org/W2100233408","https://openalex.org/W2110570734","https://openalex.org/W2115638597","https://openalex.org/W2118780696","https://openalex.org/W2123534114","https://openalex.org/W2127498940","https://openalex.org/W2141461755","https://openalex.org/W2143424400","https://openalex.org/W2144462058","https://openalex.org/W2150934173","https://openalex.org/W2964340057"],"related_works":["https://openalex.org/W2128140984","https://openalex.org/W2951509310","https://openalex.org/W1605984840","https://openalex.org/W2739728095","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2057191541","https://openalex.org/W2105489997","https://openalex.org/W2159892619","https://openalex.org/W1988675506"],"abstract_inverted_index":{"The":[0,26],"Perl":[1,27],"package":[2,28],"is":[3,19],"available":[4,21],"as":[5],"part":[6],"of":[7,32],"the":[8],"BioPerl":[9],"bundle,":[10],"and":[11,24],"can":[12],"also":[13,20],"be":[14],"downloaded.":[15],"A":[16],"web-based":[17],"application":[18],"(see":[22],"availability":[23],"requirements).":[25],"includes":[29],"full":[30],"documentation":[31],"all":[33],"its":[34],"features.":[35]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}