{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T03:58:12Z","timestamp":1785729492540,"version":"3.56.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2023,8,31]],"date-time":"2023-08-31T00:00:00Z","timestamp":1693440000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Guangdong Provincial Genomics Data Center","award":["2021B1212100001"],"award-info":[{"award-number":["2021B1212100001"]}]},{"name":"Chan-Zuckerberg"},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP200103151"],"award-info":[{"award-number":["DP200103151"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10\u200a000 sequences. Given the increasing pace of generating new sequence data, particularly in outbreaks of emerging diseases, and the already enormous existing databases of sequence data for which Neighbour-Joining is a useful approach, new implementations of existing methods are warranted.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present DecentTree, which provides highly optimized and parallel implementations of Neighbour-Joining and several of its variants. DecentTree is designed as a stand-alone application and a header-only library easily integrated with other phylogenetic software (e.g. it is integral in the popular IQ-TREE software). We show that DecentTree shows similar or improved performance over existing software (BIONJ, Quicktree, FastME, and RapidNJ), especially for handling very large alignments. For example, DecentTree is up to 6-fold faster than the fastest existing Neighbour-Joining software (e.g. RapidNJ) when generating a tree of 64\u200a000 SARS-CoV-2 genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DecentTree is open source and freely available at https:\/\/github.com\/iqtree\/decenttree. All code and data used in this analysis are available on Github (https:\/\/github.com\/asdcid\/Comparison-of-neighbour-joining-software).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad536","type":"journal-article","created":{"date-parts":[[2023,8,31]],"date-time":"2023-08-31T17:36:48Z","timestamp":1693503408000},"source":"Crossref","is-referenced-by-count":12,"title":["DecentTree: scalable Neighbour-Joining for the genomic era"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9319-450X","authenticated-orcid":false,"given":"Weiwen","family":"Wang","sequence":"first","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Barbetti","sequence":"additional","affiliation":[{"name":"School of Computing, College of Engineering and Computer Science, Australian National University , Canberra, ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Wong","sequence":"additional","affiliation":[{"name":"Ecology and Evolution, Research School of Biology, College of Science, Australian National University , Canberra, ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6334-5186","authenticated-orcid":false,"given":"Bryan","family":"Thornlow","sequence":"additional","affiliation":[{"name":"Genomics Institute, University of California Santa Cruz , Santa Cruz, CA 95064, United States"},{"name":"Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA 95064, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Russ","family":"Corbett-Detig","sequence":"additional","affiliation":[{"name":"Genomics Institute, University of California Santa Cruz , Santa Cruz, CA 95064, United States"},{"name":"Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA 95064, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5600-2900","authenticated-orcid":false,"given":"Yatish","family":"Turakhia","sequence":"additional","affiliation":[{"name":"Electrical and Computer Engineering, University of California San Diego , La Jolla, CA 92093, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1140-2596","authenticated-orcid":false,"given":"Robert","family":"Lanfear","sequence":"additional","affiliation":[{"name":"Ecology and Evolution, Research School of Biology, College of Science, Australian National University , Canberra, ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5535-6560","authenticated-orcid":false,"given":"Bui Quang","family":"Minh","sequence":"additional","affiliation":[{"name":"School of Computing, College of Engineering and Computer Science, Australian National University , Canberra, ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,8,31]]},"reference":[{"key":"2023090906502030300_btad536-B1","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023090906502030300_btad536-B2","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1093\/oxfordjournals.molbev.a025808","article-title":"BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data","volume":"14","author":"Gascuel","year":"1997","journal-title":"Mol Biol 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