{"id":"https://openalex.org/W4360992126","doi":"https://doi.org/10.1186/s13040-023-00329-x","title":"Reference-free phylogeny from sequencing data","display_name":"Reference-free phylogeny from sequencing data","publication_year":2023,"publication_date":"2023-03-27","ids":{"openalex":"https://openalex.org/W4360992126","doi":"https://doi.org/10.1186/s13040-023-00329-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/36973746"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-023-00329-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-023-00329-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-023-00329-x","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-023-00329-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089537120","display_name":"Petr Ry\u0161av\u00fd","orcid":"https://orcid.org/0000-0002-6597-6616"},"institutions":[{"id":"https://openalex.org/I44504214","display_name":"Czech Technical University in Prague","ror":"https://ror.org/03kqpb082","country_code":"CZ","type":"education","lineage":["https://openalex.org/I44504214"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Petr Ry\u0161av\u00fd","raw_affiliation_strings":["Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic. petr.rysavy@fel.cvut.cz","Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0002-6597-6616","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic. petr.rysavy@fel.cvut.cz","institution_ids":["https://openalex.org/I44504214"]},{"raw_affiliation_string":"Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic","institution_ids":["https://openalex.org/I44504214"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062388770","display_name":"Filip \u017delezn\u00fd","orcid":"https://orcid.org/0000-0001-9780-3376"},"institutions":[{"id":"https://openalex.org/I44504214","display_name":"Czech Technical University in Prague","ror":"https://ror.org/03kqpb082","country_code":"CZ","type":"education","lineage":["https://openalex.org/I44504214"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Filip \u017delezn\u00fd","raw_affiliation_strings":["Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0001-9780-3376","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic","institution_ids":["https://openalex.org/I44504214"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5089537120"],"corresponding_institution_ids":["https://openalex.org/I44504214"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1492,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56758072,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"16","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9672999978065491,"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":0.9672999978065491,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.00930000003427267,"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":0.002400000113993883,"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/computer-science","display_name":"Computer science","score":0.6159603595733643},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5777201056480408},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45822274684906006},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42053917050361633},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.39560335874557495},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35305821895599365},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2347811460494995},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10374772548675537}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6159603595733643},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5777201056480408},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45822274684906006},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42053917050361633},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39560335874557495},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35305821895599365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2347811460494995},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10374772548675537},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-023-00329-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-023-00329-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-023-00329-x","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:36973746","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36973746","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":"BioData mining","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10045052","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10045052","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10045052/pdf/13040_2023_Article_329.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:58df942742954baebac287bb3ef44c89","is_oa":true,"landing_page_url":"https://doaj.org/article/58df942742954baebac287bb3ef44c89","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 16, Iss 1, Pp 1-20 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-023-00329-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-023-00329-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-023-00329-x","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G2291329386","display_name":null,"funder_award_id":"CZ.02.1.01/0.0/0.0/16_019/0000765","funder_id":"https://openalex.org/F4320334253","funder_display_name":"Research Center for Informatics, Czech Technical University in Prague"},{"id":"https://openalex.org/G718049477","display_name":null,"funder_award_id":"CZ.02.1.01/0.0/0.0/16_019/0000765","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G8470341104","display_name":null,"funder_award_id":"CZ.02.1.01/0.0/0.0/16_019/","funder_id":"https://openalex.org/F4320334253","funder_display_name":"Research Center for Informatics, Czech Technical University in Prague"}],"funders":[{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320334253","display_name":"Research Center for Informatics, Czech Technical University in Prague","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4360992126.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1966822396","https://openalex.org/W1968363797","https://openalex.org/W1970026646","https://openalex.org/W1975375203","https://openalex.org/W1999727705","https://openalex.org/W2001496424","https://openalex.org/W2006075770","https://openalex.org/W2011632873","https://openalex.org/W2023911006","https://openalex.org/W2030644393","https://openalex.org/W2036145579","https://openalex.org/W2043481183","https://openalex.org/W2048124712","https://openalex.org/W2050711351","https://openalex.org/W2074231493","https://openalex.org/W2080718774","https://openalex.org/W2097706568","https://openalex.org/W2099964107","https://openalex.org/W2104549677","https://openalex.org/W2105875994","https://openalex.org/W2119488386","https://openalex.org/W2120358246","https://openalex.org/W2150698190","https://openalex.org/W2157539385","https://openalex.org/W2160969485","https://openalex.org/W2166162901","https://openalex.org/W2171475724","https://openalex.org/W2224150270","https://openalex.org/W2523724266","https://openalex.org/W2618826046","https://openalex.org/W2754651556","https://openalex.org/W2761430568","https://openalex.org/W2763485408","https://openalex.org/W2790276913","https://openalex.org/W2950150251","https://openalex.org/W2963017196","https://openalex.org/W3112750589"],"related_works":["https://openalex.org/W158575883","https://openalex.org/W1967721632","https://openalex.org/W2155276701","https://openalex.org/W2076755063","https://openalex.org/W4213212078","https://openalex.org/W4238308242","https://openalex.org/W2086569686","https://openalex.org/W2086773790","https://openalex.org/W1594188133","https://openalex.org/W2744549373"],"abstract_inverted_index":{"MOTIVATION:":[0],"Clustering":[1],"of":[2,7,11,28,39,55,89,110,118,131,143,152,168],"genetic":[3],"sequences":[4],"is":[5,96],"one":[6],"the":[8,26,33,44,52,108,111,119,123,129,134,138,141,144,153],"key":[9],"parts":[10],"bioinformatics":[12],"analyses.":[13],"Resulting":[14],"phylogenetic":[15],"trees":[16],"are":[17,65],"beneficial":[18],"for":[19,85,103,161],"solving":[20],"many":[21],"research":[22],"questions,":[23],"including":[24],"tracing":[25,36],"history":[27],"species,":[29],"studying":[30],"migration":[31],"in":[32,51,126,147],"past,":[34],"or":[35,57],"a":[37,40,83,148,158],"source":[38],"virus":[41],"outbreak.":[42],"At":[43],"same":[45],"time,":[46],"biologists":[47],"provide":[48],"more":[49],"data":[50,70,91],"raw":[53,104],"form":[54],"reads":[56],"only":[58],"on":[59],"contig-level":[60],"assembly.":[61],"Therefore,":[62],"tools":[63],"that":[64],"able":[66],"to":[67,74,137],"process":[68],"those":[69],"without":[71],"supervision":[72],"need":[73],"be":[75],"developed.":[76],"RESULTS:":[77],"In":[78],"this":[79],"paper,":[80],"we":[81],"present":[82],"tool":[84,99,114],"reference-free":[86],"phylogeny":[87],"capable":[88],"handling":[90],"where":[92],"no":[93],"mature-level":[94],"assembly":[95],"available.":[97],"The":[98,113],"allows":[100],"distance":[101,121],"calculation":[102],"reads,":[105],"contigs,":[106],"and":[107,155,164],"combination":[109,151],"latter.":[112],"provides":[115],"an":[116,165],"estimation":[117],"Levenshtein":[120],"between":[122,133],"sequences,":[124],"which":[125],"turn":[127],"estimates":[128],"number":[130],"mutations":[132],"organisms.":[135],"Compared":[136],"previous":[139],"research,":[140],"novelty":[142],"method":[145,160],"lies":[146],"newly":[149],"proposed":[150],"read":[154],"contig":[156],"measures,":[157],"new":[159],"read-contig":[162],"mapping,":[163],"efficient":[166],"embedding":[167],"contigs.":[169]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}