{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:07:04Z","timestamp":1788826024428,"version":"build-2803163510"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T00:00:00Z","timestamp":1594166400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"US Department of Energy (DOE) Joint Genome Institute, an Office of Science User Facility"},{"name":"Office of Science of the US Department of Energy","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}]},{"name":"Facilities Integrating Collaborations for User Science"},{"DOI":"10.13039\/100015911","name":"JGI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015911","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017223","name":"NERSC","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100017223","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Genome British Columbia; Genome Canada"},{"DOI":"10.13039\/100013020","name":"Compute Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013020","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Koonkie Inc"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TreeSAPP was developed in Python 3 as an open-source Python package and is available on GitHub at https:\/\/github.com\/hallamlab\/TreeSAPP.<\/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\/btaa588","type":"journal-article","created":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T03:20:23Z","timestamp":1593573623000},"page":"4706-4713","source":"Crossref","is-referenced-by-count":9,"title":["TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6714-0898","authenticated-orcid":false,"given":"Connor","family":"Morgan-Lang","sequence":"first","affiliation":[{"name":"Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre , Vancouver, British Columbia V5Z 4S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"McLaughlin","sequence":"additional","affiliation":[{"name":"Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre , Vancouver, British Columbia V5Z 4S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary","family":"Armstrong","sequence":"additional","affiliation":[{"name":"Genome Science and Technology Program, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, University of British Columbia , Vancouver BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Chan","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, University of British Columbia , Vancouver BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven J","family":"Hallam","sequence":"additional","affiliation":[{"name":"Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre , Vancouver, British Columbia V5Z 4S6, Canada"},{"name":"Genome Science and Technology Program, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"},{"name":"Department of Electrical and Computer Engineering, University of British Columbia , Vancouver BC V6T 1Z4, Canada"},{"name":"Department of Microbiology and Immunology, University of British Columbia , 2552-2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada"},{"name":"ECOSCOPE Training Program, University of British Columbia , Vancouver, British Columbia V6T 1Z, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,7,8]]},"reference":[{"key":"2023062213565494600_btaa588-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023062213565494600_btaa588-B2","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/sysbio\/syy054","article-title":"EPA-ng: massively parallel evolutionary placement of genetic sequences","volume":"68","author":"Barbera","year":"2019","journal-title":"Syst. Biol"},{"key":"2023062213565494600_btaa588-B3","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btr320","article-title":"Aligning short reads to reference alignments and trees","volume":"27","author":"Berger","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B4","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1186\/1471-2164-15-679","article-title":"Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine","volume":"15","author":"Borrel","year":"2014","journal-title":"BMC Genomics"},{"key":"2023062213565494600_btaa588-B5","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/s41564-019-0363-3","article-title":"Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea","volume":"4","author":"Borrel","year":"2019","journal-title":"Nat. Microbiol"},{"key":"2023062213565494600_btaa588-B6","doi-asserted-by":"crossref","first-page":"e0177678","DOI":"10.1371\/journal.pone.0177678","article-title":"Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric","volume":"12","author":"Boughorbel","year":"2017","journal-title":"PLoS One"},{"key":"2023062213565494600_btaa588-B7","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1093\/nar\/gky174","article-title":"GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes","volume":"46","author":"Boyd","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062213565494600_btaa588-B8","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"2023062213565494600_btaa588-B9","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1126\/science.1186120","article-title":"The evolution and future of earth\u2019s nitrogen cycle","volume":"330","author":"Canfield","year":"2010","journal-title":"Science"},{"key":"2023062213565494600_btaa588-B10","first-page":"1","article-title":"GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database","volume":"36","author":"Chaumeil","year":"2019","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B11","doi-asserted-by":"crossref","DOI":"10.1126\/science.1123061","article-title":"Toward automatic reconstruction of a highly resolved tree of life","author":"Ciccarelli","year":"2006"},{"key":"2023062213565494600_btaa588-B12","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B13","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1186\/1471-2148-10-210","article-title":"BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments","volume":"10","author":"Criscuolo","year":"2010","journal-title":"BMC Evol. Biol"},{"key":"2023062213565494600_btaa588-B14","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1038\/s41587-019-0260-6","article-title":"Targeted isolation and cultivation of uncultivated bacteria by reverse genomics","volume":"37","author":"Cross","year":"2019","journal-title":"Nat. Biotechnol"},{"key":"2023062213565494600_btaa588-B15","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1093\/bioinformatics\/bty767","article-title":"Methods for automatic reference trees and multilevel phylogenetic placement","volume":"35","author":"Czech","year":"2019","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B16","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":"2023062213565494600_btaa588-B17","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B18","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B19","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/s41579-018-0136-7","article-title":"An evolving view of methane metabolism in the Archaea","volume":"17","author":"Evans","year":"2019","journal-title":"Nat. Rev. Microbiol"},{"key":"2023062213565494600_btaa588-B20","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1126\/science.1153213","article-title":"The microbial engines that drive earth\u2019s biogeochemical cycles","volume":"320","author":"Falkowski","year":"2008","journal-title":"Science"},{"key":"2023062213565494600_btaa588-B21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2013.00291","article-title":"FunGene: the functional gene pipeline and repository","volume":"4","author":"Fish","year":"2013","journal-title":"Front. Microbiol"},{"key":"2023062213565494600_btaa588-B22","doi-asserted-by":"crossref","first-page":"3535","DOI":"10.1093\/bioinformatics\/btw400","article-title":"LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes","volume":"32","author":"Hanson","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B23","doi-asserted-by":"crossref","first-page":"4574","DOI":"10.1038\/s41467-019-12574-y","article-title":"Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea","volume":"10","author":"Hua","year":"2019","journal-title":"Nat. Commun"},{"key":"2023062213565494600_btaa588-B24","doi-asserted-by":"crossref","first-page":"D286","DOI":"10.1093\/nar\/gkv1248","article-title":"eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences","volume":"44","author":"Huerta-Cepas","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023062213565494600_btaa588-B25","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/molbev\/msw046","article-title":"ETE 3: reconstruction, analysis, and visualization of phylogenomic data","volume":"33","author":"Huerta-Cepas","year":"2016","journal-title":"Mol. Biol. Evol"},{"key":"2023062213565494600_btaa588-B26","doi-asserted-by":"crossref","first-page":"R123","DOI":"10.1186\/gb-2013-14-11-r123","article-title":"Metabolic reprogramming by viruses in the sunlit and dark ocean","volume":"14","author":"Hurwitz","year":"2013","journal-title":"Genome Biol"},{"key":"2023062213565494600_btaa588-B27","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1101\/gr.5969107","article-title":"MEGAN analysis of metagenomic data","volume":"17","author":"Huson","year":"2007","journal-title":"Genome Res"},{"key":"2023062213565494600_btaa588-B28","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023062213565494600_btaa588-B29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-015-0702-1","article-title":"OD-seq: outlier detection in multiple sequence alignments","volume":"16","author":"Jehl","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2023062213565494600_btaa588-B30","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol"},{"key":"2023062213565494600_btaa588-B31","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res"},{"key":"2023062213565494600_btaa588-B32","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1186\/1471-2105-14-202","article-title":"MetaPathways: a modular pipeline for constructing pathway\/genome databases from environmental sequence information","volume":"14","author":"Konwar","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023062213565494600_btaa588-B33","doi-asserted-by":"crossref","first-page":"5022","DOI":"10.1093\/nar\/gkw396","article-title":"Phylogeny-aware identification and correction of taxonomically mislabeled sequences","volume":"44","author":"Kozlov","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023062213565494600_btaa588-B34","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","article-title":"RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference","volume":"35","author":"Kozlov","year":"2019","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B35","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1038\/nature20152","article-title":"Thermophilic archaea activate butane via alkyl-coenzyme M formation","volume":"539","author":"Laso-P\u00e9rez","year":"2016","journal-title":"Nature"},{"key":"2023062213565494600_btaa588-B36","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"Le","year":"2008","journal-title":"Mol. Biol. Evol"},{"key":"2023062213565494600_btaa588-B37","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees","volume":"44","author":"Letunic","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023062213565494600_btaa588-B38","doi-asserted-by":"crossref","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree Of Life (iTOL) v4: recent updates and new developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023062213565494600_btaa588-B39","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":"2023062213565494600_btaa588-B40","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","article-title":"Comparison of the predicted and observed secondary structure of T4 phage lysozyme","volume":"405","author":"Matthews","year":"1975","journal-title":"Biochim. Biophys. Acta"},{"key":"2023062213565494600_btaa588-B41","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1038\/s41564-019-0362-4","article-title":"Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota","volume":"4","author":"McKay","year":"2019","journal-title":"Nat. Microbiol"},{"key":"2023062213565494600_btaa588-B42","doi-asserted-by":"crossref","first-page":"e675","DOI":"10.7717\/peerj.675","article-title":"Unexpected cross-species contamination in genome sequencing projects","volume":"2","author":"Merchant","year":"2014","journal-title":"PeerJ"},{"key":"2023062213565494600_btaa588-B43","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1038\/ismej.2014.208","article-title":"Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases","volume":"9","author":"M\u00fcller","year":"2015","journal-title":"ISME J"},{"key":"2023062213565494600_btaa588-B44","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-018-1554-6","article-title":"RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification","volume":"19","author":"Nasko","year":"2018","journal-title":"Genome Biol"},{"key":"2023062213565494600_btaa588-B45","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1128\/AEM.01754-09","article-title":"Use of ichip for high-throughput in situ cultivation of \u201cuncultivable microbial species\u201d","volume":"76","author":"Nichols","year":"2010","journal-title":"Appl. Environ. Microbiol"},{"key":"2023062213565494600_btaa588-B46","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol"},{"key":"2023062213565494600_btaa588-B47","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nbt.4229","article-title":"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life","volume":"36","author":"Parks","year":"2018","journal-title":"Nat. Biotechnol"},{"key":"2023062213565494600_btaa588-B48","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1089\/cmb.2009.0179","article-title":"How many bootstrap replicates are necessary?","volume":"17","author":"Pattengale","year":"2010","journal-title":"J. Comput. Biol"},{"key":"2023062213565494600_btaa588-B49","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1186\/s12859-015-0788-5","article-title":"Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities","volume":"16","author":"Peabody","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2023062213565494600_btaa588-B50","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 - approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"2023062213565494600_btaa588-B51","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1146\/annurev.micro.57.030502.090759","article-title":"The uncultured microbial majority","volume":"57","author":"Rapp\u00e9","year":"2003","journal-title":"Annu. Rev. Microbiol"},{"key":"2023062213565494600_btaa588-B52","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nature12352","article-title":"Insights into the phylogeny and coding potential of microbial dark matter","volume":"499","author":"Rinke","year":"2013","journal-title":"Nature"},{"key":"2023062213565494600_btaa588-B53","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1038\/nmeth.4458","article-title":"Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software","volume":"14","author":"Sczyrba","year":"2017","journal-title":"Nat. Methods"},{"key":"2023062213565494600_btaa588-B54","doi-asserted-by":"crossref","first-page":"1822","DOI":"10.1038\/s41467-019-09364-x","article-title":"Asgard archaea capable of anaerobic hydrocarbon cycling","volume":"10","author":"Seitz","year":"2019","journal-title":"Nat. Commun"},{"key":"2023062213565494600_btaa588-B55","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.00725-19","article-title":"Composite metagenome-assembled genomes reduce the quality of public genome repositories","volume":"10","author":"Shaiber","year":"2019","journal-title":"mBio"},{"key":"2023062213565494600_btaa588-B56","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.mib.2016.04.020","article-title":"The bright side of microbial dark matter: lessons learned from the uncultivated majority","volume":"31","author":"Solden","year":"2016","journal-title":"Curr. Opin. Microbiol"},{"key":"2023062213565494600_btaa588-B57","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1099\/00207713-45-3-554","article-title":"Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae","volume":"45","author":"Springer","year":"1995","journal-title":"Int. J. Syst. Bacteriol"},{"key":"2023062213565494600_btaa588-B58","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B59","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1186\/1471-2164-11-461","article-title":"MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies","volume":"11","author":"Stark","year":"2010","journal-title":"BMC Genomics"},{"key":"2023062213565494600_btaa588-B60","doi-asserted-by":"crossref","first-page":"3126","DOI":"10.1038\/s41396-019-0484-y","article-title":"High proportions of bacteria and archaea across most biomes remain uncultured","volume":"13","author":"Steen","year":"2019","journal-title":"ISME J"},{"key":"2023062213565494600_btaa588-B61","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1093\/sysbio\/syv033","article-title":"Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference","volume":"64","author":"Tan","year":"2015","journal-title":"Syst. Biol"},{"key":"2023062213565494600_btaa588-B62","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41564-019-0364-2","article-title":"Expanding anaerobic alkane metabolism in the domain of Archaea","volume":"4","author":"Wang","year":"2019","journal-title":"Nat. Microbiol"},{"key":"2023062213565494600_btaa588-B63","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/0-387-30743-5_9","volume-title":"Prokaryotes","author":"Whitman","year":"2006"},{"key":"2023062213565494600_btaa588-B64","doi-asserted-by":"crossref","first-page":"2702","DOI":"10.1093\/bioinformatics\/btw241","article-title":"OrfM: A fast open reading frame predictor for metagenomic data","volume":"32","author":"Woodcroft","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062213565494600_btaa588-B65","article-title":"TreeOTU: operational taxonomic unit classification based on phylogenetic trees","author":"Wu","year":"2013","journal-title":"Preprint at https:\/\/arxiv.org\/abs\/1308.6333."},{"key":"2023062213565494600_btaa588-B66","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.cell.2019.07.010","article-title":"Benchmarking metagenomics tools for taxonomic classification","volume":"178","author":"Ye","year":"2019","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa588\/33979426\/btaa588.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/18\/4706\/50677698\/btaa588.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/18\/4706\/50677698\/btaa588.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T20:22:07Z","timestamp":1687551727000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/18\/4706\/5868555"}},"subtitle":[],"editor":[{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,7,8]]},"references-count":66,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2020,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa588","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,9,15]]},"published":{"date-parts":[[2020,7,8]]}}}