{"id":"https://openalex.org/W4404607640","doi":"https://doi.org/10.1093/bioinformatics/btae701","title":"Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix","display_name":"Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix","publication_year":2024,"publication_date":"2024-11-21","ids":{"openalex":"https://openalex.org/W4404607640","doi":"https://doi.org/10.1093/bioinformatics/btae701","pmid":"https://pubmed.ncbi.nlm.nih.gov/39570613"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae701","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btae701","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018918290","display_name":"Semih Kurt","orcid":"https://orcid.org/0000-0002-9760-9140"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Semih Kurt","raw_affiliation_strings":["School of EECS and SciLifeLab, KTH Royal Institute of Technology , Stockholm, 100 44,","School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"School of EECS and SciLifeLab, KTH Royal Institute of Technology , Stockholm, 100 44,","institution_ids":["https://openalex.org/I86987016"]},{"raw_affiliation_string":"School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016","https://openalex.org/I2800139495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003426513","display_name":"Alexandre Bouchard\u2010C\u00f4t\u00e9","orcid":"https://orcid.org/0000-0001-7402-8506"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alexandre Bouchard-C\u00f4t\u00e9","raw_affiliation_strings":["Department of Statistics, University of British Columbia , Vancouver, BC, V6T 1Z4,","Department of Statistics, University of British Columbia, Vancouver, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of British Columbia , Vancouver, BC, V6T 1Z4,","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Department of Statistics, University of British Columbia, Vancouver, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064553103","display_name":"Jens Lagergren","orcid":"https://orcid.org/0000-0002-4552-0240"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jens Lagergren","raw_affiliation_strings":["School of EECS and SciLifeLab, KTH Royal Institute of Technology , Stockholm, 100 44,","School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"School of EECS and SciLifeLab, KTH Royal Institute of Technology , Stockholm, 100 44,","institution_ids":["https://openalex.org/I86987016"]},{"raw_affiliation_string":"School of EECS and SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016","https://openalex.org/I2800139495"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5018918290"],"corresponding_institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I86987016"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.229,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59045802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"40","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":0.9995999932289124,"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":0.9995999932289124,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9786999821662903,"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":0.9616000056266785,"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/distance-matrix","display_name":"Distance matrix","score":0.7918300628662109},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7526123523712158},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7001489400863647},{"id":"https://openalex.org/keywords/sparse-matrix","display_name":"Sparse matrix","score":0.5422161817550659},{"id":"https://openalex.org/keywords/distance-matrices-in-phylogeny","display_name":"Distance matrices in phylogeny","score":0.5414775013923645},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5335728526115417},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5205410718917847},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.48066914081573486},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.46683064103126526},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45978620648384094},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.437540203332901},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4173663258552551},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3872324526309967},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32567447423934937},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.2607883810997009},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22889426350593567},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20814639329910278},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08104977011680603}],"concepts":[{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.7918300628662109},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7526123523712158},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7001489400863647},{"id":"https://openalex.org/C56372850","wikidata":"https://www.wikidata.org/wiki/Q1050404","display_name":"Sparse matrix","level":3,"score":0.5422161817550659},{"id":"https://openalex.org/C5349765","wikidata":"https://www.wikidata.org/wiki/Q5282866","display_name":"Distance matrices in phylogeny","level":2,"score":0.5414775013923645},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5335728526115417},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5205410718917847},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.48066914081573486},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.46683064103126526},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45978620648384094},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.437540203332901},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4173663258552551},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3872324526309967},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32567447423934937},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.2607883810997009},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22889426350593567},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20814639329910278},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08104977011680603},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae701","pdf_url":null,"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:39570613","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39570613","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11637600","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11637600","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11637600/pdf/btae701.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae701","pdf_url":null,"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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.47999998927116394}],"awards":[{"id":"https://openalex.org/G5733910190","display_name":null,"funder_award_id":"2018-06217_VR","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G6064834762","display_name":null,"funder_award_id":"2022-03516_VR","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G712881263","display_name":null,"funder_award_id":"2018-","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1554271130","https://openalex.org/W1600438564","https://openalex.org/W1996835973","https://openalex.org/W2017930713","https://openalex.org/W2028715154","https://openalex.org/W2031611770","https://openalex.org/W2035831318","https://openalex.org/W2038876634","https://openalex.org/W2060425093","https://openalex.org/W2079970266","https://openalex.org/W2083700194","https://openalex.org/W2108531996","https://openalex.org/W2109586018","https://openalex.org/W2114055146","https://openalex.org/W2129816388","https://openalex.org/W2132926880","https://openalex.org/W2142056356","https://openalex.org/W2407405674","https://openalex.org/W2750791471","https://openalex.org/W2801900613","https://openalex.org/W2889178232","https://openalex.org/W2952045272","https://openalex.org/W2952384398","https://openalex.org/W2963132458","https://openalex.org/W2963464696","https://openalex.org/W3005235420","https://openalex.org/W3016794363","https://openalex.org/W3162593345","https://openalex.org/W4239634997","https://openalex.org/W4292572940","https://openalex.org/W4310491011","https://openalex.org/W4363675392","https://openalex.org/W4379352616","https://openalex.org/W4387674331","https://openalex.org/W6643380523","https://openalex.org/W6649753774"],"related_works":["https://openalex.org/W2001076853","https://openalex.org/W1872375678","https://openalex.org/W4387171312","https://openalex.org/W4388316203","https://openalex.org/W4206923957","https://openalex.org/W4235784610","https://openalex.org/W4236196889","https://openalex.org/W1605858995","https://openalex.org/W2090844285","https://openalex.org/W1753959406"],"abstract_inverted_index":{"Sparse":[0],"Neighbor":[1],"Joining":[2],"is":[3],"implemented":[4],"in":[5],"Python":[6],"and":[7],"freely":[8],"available":[9],"at":[10],"https://github.com/kurtsemih/SNJ.":[11]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}