{"id":"https://openalex.org/W4416376992","doi":"https://doi.org/10.1093/bioinformatics/btaf620","title":"<tt>raxtax</tt> : a <i>k</i> -mer-based non-Bayesian taxonomic classifier","display_name":"<tt>raxtax</tt> : a <i>k</i> -mer-based non-Bayesian taxonomic classifier","publication_year":2025,"publication_date":"2025-11-17","ids":{"openalex":"https://openalex.org/W4416376992","doi":"https://doi.org/10.1093/bioinformatics/btaf620","pmid":"https://pubmed.ncbi.nlm.nih.gov/41259660"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf620","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf620","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf620/65397086/btaf620.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf620/65397086/btaf620.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104488470","display_name":"Noah A Wahl","orcid":"https://orcid.org/0009-0001-7628-6557"},"institutions":[{"id":"https://openalex.org/I8901234","display_name":"Foundation for Research and Technology Hellas","ror":"https://ror.org/052rphn09","country_code":"GR","type":"facility","lineage":["https://openalex.org/I8901234"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Noah A Wahl","raw_affiliation_strings":["Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece"],"affiliations":[{"raw_affiliation_string":"Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","institution_ids":["https://openalex.org/I8901234"]},{"raw_affiliation_string":"Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece","institution_ids":["https://openalex.org/I8901234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081879046","display_name":"Georgios Koutsovoulos","orcid":"https://orcid.org/0000-0003-3406-3715"},"institutions":[{"id":"https://openalex.org/I8901234","display_name":"Foundation for Research and Technology Hellas","ror":"https://ror.org/052rphn09","country_code":"GR","type":"facility","lineage":["https://openalex.org/I8901234"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Georgios Koutsovoulos","raw_affiliation_strings":["Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece"],"affiliations":[{"raw_affiliation_string":"Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","institution_ids":["https://openalex.org/I8901234"]},{"raw_affiliation_string":"Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece","institution_ids":["https://openalex.org/I8901234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046240335","display_name":"Ben Bettisworth","orcid":"https://orcid.org/0000-0002-9130-6878"},"institutions":[{"id":"https://openalex.org/I8901234","display_name":"Foundation for Research and Technology Hellas","ror":"https://ror.org/052rphn09","country_code":"GR","type":"facility","lineage":["https://openalex.org/I8901234"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Ben Bettisworth","raw_affiliation_strings":["Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece"],"affiliations":[{"raw_affiliation_string":"Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","institution_ids":["https://openalex.org/I8901234"]},{"raw_affiliation_string":"Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece","institution_ids":["https://openalex.org/I8901234"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025640090","display_name":"Alexandros Stamatakis","orcid":"https://orcid.org/0000-0003-0353-0691"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]},{"id":"https://openalex.org/I71030271","display_name":"Heidelberg Institute for Theoretical Studies","ror":"https://ror.org/01f7bcy98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I71030271"]},{"id":"https://openalex.org/I8901234","display_name":"Foundation for Research and Technology Hellas","ror":"https://ror.org/052rphn09","country_code":"GR","type":"facility","lineage":["https://openalex.org/I8901234"]}],"countries":["DE","GR"],"is_corresponding":false,"raw_author_name":"Alexandros Stamatakis","raw_affiliation_strings":["Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","Heidelberg Institute for Theoretical Studies Computational Molecular Evolution Group, , Schlo\u00df-Wolfsbrunnenweg 35 , Heidelberg, Baden-W\u00fcrttemberg, 69118,","Karlsruhe Institute of Technology Institute of Theoretical Informatics, , Kaiserstra\u00dfe 12 , Karlsruhe, Baden-W\u00fcrttemberg, 76131,","Institute for Theoretical Informatics, Karlsruhe Institute of Technology , Karlsruhe, Baden-W\u00fcrttemberg 76131,","Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece","Heidelberg Institute for Theoretical Studies Computational Molecular Evolution Group, , Heidelberg, Baden-W\u00fcrttemberg 69118,"],"affiliations":[{"raw_affiliation_string":"Foundation for Research and Technology Hellas Biodiversity Computing Group, Institute of Computer Science, , N. Plastira 100 , Heraklion, Crete, 70013,","institution_ids":["https://openalex.org/I8901234"]},{"raw_affiliation_string":"Heidelberg Institute for Theoretical Studies Computational Molecular Evolution Group, , Schlo\u00df-Wolfsbrunnenweg 35 , Heidelberg, Baden-W\u00fcrttemberg, 69118,","institution_ids":["https://openalex.org/I71030271"]},{"raw_affiliation_string":"Karlsruhe Institute of Technology Institute of Theoretical Informatics, , Kaiserstra\u00dfe 12 , Karlsruhe, Baden-W\u00fcrttemberg, 76131,","institution_ids":["https://openalex.org/I102335020"]},{"raw_affiliation_string":"Institute for Theoretical Informatics, Karlsruhe Institute of Technology , Karlsruhe, Baden-W\u00fcrttemberg 76131,","institution_ids":["https://openalex.org/I102335020"]},{"raw_affiliation_string":"Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece","institution_ids":["https://openalex.org/I8901234"]},{"raw_affiliation_string":"Heidelberg Institute for Theoretical Studies Computational Molecular Evolution Group, , Heidelberg, Baden-W\u00fcrttemberg 69118,","institution_ids":["https://openalex.org/I71030271"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5104488470"],"corresponding_institution_ids":["https://openalex.org/I8901234"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.31444729,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5501000285148621,"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":0.5501000285148621,"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/T10895","display_name":"Species Distribution and Climate Change","score":0.09510000050067902,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.05700000002980232,"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/classifier","display_name":"Classifier (UML)","score":0.5835000276565552},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5115000009536743},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.4235000014305115},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.3937999904155731}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6841999888420105},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6438999772071838},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5835000276565552},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5115000009536743},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.4235000014305115},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3937999904155731},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2971999943256378},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2750999927520752},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2581000030040741}],"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":"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058893","descriptor_name":"DNA Barcoding, Taxonomic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaf620","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf620","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf620/65397086/btaf620.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41259660","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41259660","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf620","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf620","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf620/65397086/btaf620.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G40230781","display_name":null,"funder_award_id":"101087081","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416376992.pdf","grobid_xml":"https://content.openalex.org/works/W4416376992.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1857789879","https://openalex.org/W1966913051","https://openalex.org/W2099901798","https://openalex.org/W2102917628","https://openalex.org/W2110375946","https://openalex.org/W2128591967","https://openalex.org/W2152885278","https://openalex.org/W2171405751","https://openalex.org/W2295825336","https://openalex.org/W2496540622","https://openalex.org/W2745994342","https://openalex.org/W2886687368","https://openalex.org/W2898103936","https://openalex.org/W2990618091","https://openalex.org/W3121953277","https://openalex.org/W4311058533","https://openalex.org/W4385302437","https://openalex.org/W4388637778","https://openalex.org/W4403138369"],"related_works":[],"abstract_inverted_index":{"raxtax":[0],"is":[1],"available":[2,19,34],"at":[3,20,35],"https://github.com/noahares/raxtax":[4],"under":[5],"a":[6],"CC-NC-BY-SA":[7],"license.":[8],"The":[9,22],"scripts":[10],"and":[11,27],"summary":[12],"metrics":[13],"used":[14],"in":[15],"our":[16],"analyses":[17,32],"are":[18,33],"https://github.com/noahares/raxtax_paper_scripts.":[21],"source":[23],"code,":[24],"sequence":[25],"data,":[26],"summarized":[28],"results":[29],"of":[30],"the":[31],"https://doi.org/10.5281/zenodo.15057027.":[36]},"counts_by_year":[],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-11-20T00:00:00"}
