{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T00:40:07Z","timestamp":1783730407933,"version":"3.55.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":692,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.<\/jats:p>\n               <jats:p>Results: \u00a0Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6\u2009Gb of sequence data per day on a standard multiprocessor system with 10\u2009CPU cores and microbial RefSeq as the genomic reference data.<\/jats:p>\n               <jats:p>Availability and implementation: Taxator-tk source and binary program files are publicly available at http:\/\/algbio.cs.uni-duesseldorf.de\/software\/.<\/jats:p>\n               <jats:p>Contact: \u00a0Alice.McHardy@uni-duesseldorf.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu745","type":"journal-article","created":{"date-parts":[[2014,11,12]],"date-time":"2014-11-12T04:44:24Z","timestamp":1415767464000},"page":"817-824","source":"Crossref","is-referenced-by-count":139,"title":["<i>Taxator-tk<\/i>: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods"],"prefix":"10.1093","volume":"31","author":[{"given":"J.","family":"Dr\u00f6ge","sequence":"first","affiliation":[{"name":"1 Department for Algorithmic Bioinformatics, Heinrich Heine University, Universit\u00e4tsstra\u00dfe 1, 40225 D\u00fcsseldorf, Germany, 2Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbr\u00fccken, Germany and 3Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, 38124 Braunschweig, Germany"},{"name":"1 Department for Algorithmic Bioinformatics, Heinrich Heine University, Universit\u00e4tsstra\u00dfe 1, 40225 D\u00fcsseldorf, Germany, 2Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbr\u00fccken, Germany and 3Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, 38124 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I.","family":"Gregor","sequence":"additional","affiliation":[{"name":"1 Department for Algorithmic Bioinformatics, Heinrich Heine University, Universit\u00e4tsstra\u00dfe 1, 40225 D\u00fcsseldorf, Germany, 2Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbr\u00fccken, Germany and 3Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, 38124 Braunschweig, Germany"},{"name":"1 Department for Algorithmic Bioinformatics, Heinrich Heine University, Universit\u00e4tsstra\u00dfe 1, 40225 D\u00fcsseldorf, Germany, 2Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbr\u00fccken, Germany and 3Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, 38124 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. C.","family":"McHardy","sequence":"additional","affiliation":[{"name":"1 Department for Algorithmic Bioinformatics, Heinrich Heine University, Universit\u00e4tsstra\u00dfe 1, 40225 D\u00fcsseldorf, Germany, 2Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbr\u00fccken, Germany and 3Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, 38124 Braunschweig, Germany"},{"name":"1 Department for Algorithmic Bioinformatics, Heinrich Heine University, Universit\u00e4tsstra\u00dfe 1, 40225 D\u00fcsseldorf, Germany, 2Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbr\u00fccken, Germany and 3Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, 38124 Braunschweig, Germany"},{"name":"1 Department for Algorithmic Bioinformatics, Heinrich Heine University, Universit\u00e4tsstra\u00dfe 1, 40225 D\u00fcsseldorf, Germany, 2Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbr\u00fccken, Germany and 3Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, 38124 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,11,10]]},"reference":[{"key":"2023020116180039000_btu745-B1","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nbt.2579","article-title":"Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes","volume":"31","author":"Albertsen","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2023020116180039000_btu745-B2","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat. Methods"},{"key":"2023020116180039000_btu745-B3","doi-asserted-by":"crossref","first-page":"e1002373","DOI":"10.1371\/journal.pcbi.1002373","article-title":"Joint analysis of multiple metagenomic samples","volume":"8","author":"Baran","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"2023020116180039000_btu745-B4","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1093\/sysbio\/syr010","article-title":"Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood","volume":"60","author":"Berger","year":"2011","journal-title":"Syst. Biol."},{"key":"2023020116180039000_btu745-B5","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/nmeth0511-367","article-title":"PhymmBL expanded: confidence scores, custom databases, parallelization and more","volume":"8","author":"Brady","year":"2011","journal-title":"Nat. Methods"},{"key":"2023020116180039000_btu745-B6","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020116180039000_btu745-B7","doi-asserted-by":"crossref","first-page":"e1003292","DOI":"10.1371\/journal.pcbi.1003292","article-title":"Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution","volume":"9","author":"Carr","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"2023020116180039000_btu745-B8","doi-asserted-by":"crossref","first-page":"e243","DOI":"10.7717\/peerj.243","article-title":"PhyloSift: phylogenetic analysis of genomes and metagenomes","volume":"2","author":"Darling","year":"2014","journal-title":"PeerJ"},{"key":"2023020116180039000_btu745-B9","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1093\/bib\/bbs031","article-title":"Taxonomic binning of metagenome samples generated by next-generation sequencing technologies","volume":"13","author":"Dr\u00f6ge","year":"2012","journal-title":"Brief. Bioinform."},{"key":"2023020116180039000_btu745-B10","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/1471-2105-11-80","article-title":"Parameters for accurate genome alignment","volume":"11","author":"Frith","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020116180039000_btu745-B11","doi-asserted-by":"crossref","first-page":"e91","DOI":"10.1093\/nar\/gkr225","article-title":"Taxonomic classification of metagenomic shotgun sequences with CARMA3","volume":"39","author":"Gerlach","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023020116180039000_btu745-B12","article-title":"PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes","author":"Gregor","year":"2014"},{"key":"2023020116180039000_btu745-B13","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1126\/science.1200387","article-title":"Metagenomic discovery of biomass-degrading genes and genomes from cow rumen","volume":"331","author":"Hess","year":"2011","journal-title":"Science"},{"key":"2023020116180039000_btu745-B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2002-3-2-reviews0003","article-title":"Exploring prokaryotic diversity in the genomic era","volume":"3","author":"Hugenholtz","year":"2002","journal-title":"Genome Biol."},{"key":"2023020116180039000_btu745-B15","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1101\/gr.120618.111","article-title":"Integrative analysis of environmental sequences using MEGAN4","volume":"21","author":"Huson","year":"2011","journal-title":"Genome Res."},{"key":"2023020116180039000_btu745-B16","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/bioinformatics\/bts187","article-title":"pIRS: profile-based Illumina pair-end reads simulator","volume":"28","author":"Hu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020116180039000_btu745-B17","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1126\/science.1212665","article-title":"Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota","volume":"335","author":"Iverson","year":"2012","journal-title":"Science"},{"key":"2023020116180039000_btu745-B18","doi-asserted-by":"crossref","first-page":"190","DOI":"10.4161\/bact.22111","article-title":"Next generation sequencing technologies and the changing landscape of phage genomics","volume":"2","author":"Klumpp","year":"2012","journal-title":"Bacteriophage"},{"key":"2023020116180039000_btu745-B19","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1093\/bioinformatics\/btt336","article-title":"Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing","volume":"29","author":"Koslicki","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020116180039000_btu745-B20","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1128\/MMBR.00009-08","article-title":"A bioinformatician\u2019s guide to metagenomics","volume":"72","author":"Kunin","year":"2008","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"2023020116180039000_btu745-B21","doi-asserted-by":"crossref","first-page":"e10","DOI":"10.1093\/nar\/gks803","article-title":"Metagenomic abundance estimation and diagnostic testing on species level","volume":"41","author":"Lindner","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020116180039000_btu745-B22","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/2047-217X-1-18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","author":"Luo","year":"2012","journal-title":"Gigascience"},{"key":"2023020116180039000_btu745-B23","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1186\/1471-2105-11-538","article-title":"pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree","volume":"11","author":"Matsen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020116180039000_btu745-B24","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1748-7188-7-8","article-title":"Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots","volume":"7","author":"Matsen","year":"2012","journal-title":"Algorithms Mol. Biol."},{"key":"2023020116180039000_btu745-B25","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nmeth1043","article-title":"Use of simulated data sets to evaluate the fidelity of metagenomic processing methods","volume":"4","author":"Mavromatis","year":"2007","journal-title":"Nat. Methods"},{"key":"2023020116180039000_btu745-B26","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nmeth976","article-title":"Accurate phylogenetic classification of variable-length DNA fragments","volume":"4","author":"McHardy","year":"2007","journal-title":"Nat. Methods"},{"key":"2023020116180039000_btu745-B27","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1093\/bioinformatics\/btp317","article-title":"SOrt-ITEMS: sequence orthology based approach for improved taxonomic estimation of metagenomic sequences","volume":"25","author":"Monzoorul Haque","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020116180039000_btu745-B28","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nmeth0311-191","article-title":"Taxonomic metagenome sequence assignment with structured output models","volume":"8","author":"Patil","year":"2011","journal-title":"Nat. Methods"},{"key":"2023020116180039000_btu745-B29","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1126\/science.1205760","article-title":"Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies","volume":"333","author":"Pope","year":"2011","journal-title":"Science"},{"key":"2023020116180039000_btu745-B30","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1146\/annurev.genet.38.072902.091216","article-title":"Metagenomics: genomic analysis of microbial communities","volume":"38","author":"Riesenfeld","year":"2004","journal-title":"Annu. Rev. Genet."},{"key":"2023020116180039000_btu745-B31","doi-asserted-by":"crossref","first-page":"D5","DOI":"10.1093\/nar\/gkn741","article-title":"Database resources of the National Center for Biotechnology Information","volume":"37","author":"Sayers","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020116180039000_btu745-B32","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nature11711","article-title":"Genomic variation landscape of the human gut microbiome","volume":"493","author":"Schloissnig","year":"2013","journal-title":"Nature"},{"key":"2023020116180039000_btu745-B33","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nmeth.2066","article-title":"Metagenomic microbial community profiling using unique clade-specific marker genes","volume":"9","author":"Segata","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020116180039000_btu745-B34","doi-asserted-by":"crossref","first-page":"e425","DOI":"10.7717\/peerj.425","article-title":"FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares","volume":"2","author":"Silva","year":"2014","journal-title":"PeerJ"},{"key":"2023020116180039000_btu745-B35","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1186\/1471-2164-11-461","article-title":"MLTreeMap\u2014accurate maximum likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies","volume":"11","author":"Stark","year":"2010","journal-title":"BMC Genomics"},{"key":"2023020116180039000_btu745-B36","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1038\/nmeth.2693","article-title":"Metagenomic species profiling using universal phylogenetic marker genes","volume":"10","author":"Sunagawa","year":"2013","journal-title":"Nat. Methods"},{"key":"2023020116180039000_btu745-B37","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/6\/817\/49011501\/bioinformatics_31_6_817.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/6\/817\/49011501\/bioinformatics_31_6_817.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:32:04Z","timestamp":1675297924000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/6\/817\/215163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,10]]},"references-count":37,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2015,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu745","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,3,15]]},"published":{"date-parts":[[2014,11,10]]}}}