{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T01:16:17Z","timestamp":1775265377166,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,5,7]],"date-time":"2021-05-07T00:00:00Z","timestamp":1620345600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"crossref","award":["DEB 1737898"],"award-info":[{"award-number":["DEB 1737898"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100015814","name":"Great Lakes Bioenergy Research Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015814","id-type":"DOI","asserted-by":"publisher"}]},{"name":"U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research","award":["DE-SC0018409"],"award-info":[{"award-number":["DE-SC0018409"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>CONSTAX\u2014the CONSensus TAXonomy classifier\u2014was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CONSTAX2 is available at https:\/\/github.com\/liberjul\/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https:\/\/constax.readthedocs.io\/en\/latest\/. Data and scripts associated with the manuscript are available at https:\/\/github.com\/liberjul\/CONSTAXv2_ms_code.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab347","type":"journal-article","created":{"date-parts":[[2021,5,5]],"date-time":"2021-05-05T19:04:46Z","timestamp":1620241486000},"page":"3941-3943","source":"Crossref","is-referenced-by-count":38,"title":["CONSTAX2: improved taxonomic classification of environmental DNA markers"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9941-8268","authenticated-orcid":false,"given":"Julian A","family":"Liber","sequence":"first","affiliation":[{"name":"Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA"}]},{"given":"Gregory","family":"Bonito","sequence":"additional","affiliation":[{"name":"Department of Plant Soil and Microbial Sciences, Michigan State University , East Lansing, MI 48824, USA"},{"name":"Great Lakes Bioenergy Research Center, Michigan State University , East Lansing, MI 48824, USA"}]},{"given":"Gian Maria Niccol\u00f2","family":"Benucci","sequence":"additional","affiliation":[{"name":"Department of Plant Soil and Microbial Sciences, Michigan State University , East Lansing, MI 48824, USA"},{"name":"Great Lakes Bioenergy Research Center, Michigan State University , East Lansing, MI 48824, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,5,7]]},"reference":[{"key":"2023051701222444400_btab347-B1","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1186\/s12859-015-0747-1","article-title":"SPINGO: a rapid species-classifier for microbial amplicon sequences","volume":"16","author":"Allard","year":"2015","journal-title":"BMC Bioinform"},{"key":"2023051701222444400_btab347-B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023051701222444400_btab347-B3","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s40168-018-0470-z","article-title":"Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2019s q2-feature-classifier plugin","volume":"6","author":"Bokulich","year":"2018","journal-title":"Microbiome"},{"key":"2023051701222444400_btab347-B4","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.funeco.2014.08.006","article-title":"Scraping the bottom of the barrel: are rare high throughput sequences artifacts?","volume":"13","author":"Brown","year":"2015","journal-title":"Fungal Ecol"},{"key":"2023051701222444400_btab347-B5","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.mimet.2013.08.011","article-title":"High throughput sequencing methods and analysis for microbiome research","volume":"95","author":"Di Bella","year":"2013","journal-title":"J. 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