{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T05:35:56Z","timestamp":1774935356159,"version":"3.50.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,12,21]],"date-time":"2016-12-21T00:00:00Z","timestamp":1482278400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["(DEB-1046167)"],"award-info":[{"award-number":["(DEB-1046167)"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["AEA (DEB-1045766)"],"award-info":[{"award-number":["AEA (DEB-1045766)"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["FL (DEB-1046065)"],"award-info":[{"award-number":["FL (DEB-1046065)"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["(DEB-1541418)"],"award-info":[{"award-number":["(DEB-1541418)"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["AEA (DEB-1541496)"],"award-info":[{"award-number":["AEA (DEB-1541496)"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DBI-1262628"],"award-info":[{"award-number":["DBI-1262628"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["(TG-DEB090011)"],"award-info":[{"award-number":["(TG-DEB090011)"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi\u2014Pezizomycotina (Ascomycota)\u2014based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>T-BAS Version 1.0 is available online at http:\/\/tbas.hpc.ncsu.edu. Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw808","type":"journal-article","created":{"date-parts":[[2016,12,15]],"date-time":"2016-12-15T22:11:40Z","timestamp":1481839900000},"page":"1160-1168","source":"Crossref","is-referenced-by-count":72,"title":["T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life"],"prefix":"10.1093","volume":"33","author":[{"given":"Ignazio","family":"Carbone","sequence":"first","affiliation":[{"name":"Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA"}]},{"given":"James B","family":"White","sequence":"additional","affiliation":[{"name":"Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA"}]},{"given":"Jolanta","family":"Miadlikowska","sequence":"additional","affiliation":[{"name":"Department of Biology, Duke University, Durham, NC, USA"}]},{"given":"A Elizabeth","family":"Arnold","sequence":"additional","affiliation":[{"name":"School of Plant Sciences, The University of Arizona, Tucson, AZ, USA"},{"name":"Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA"}]},{"given":"Mark A","family":"Miller","sequence":"additional","affiliation":[{"name":"San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA"}]},{"given":"Frank","family":"Kauff","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Giessen, Giessen, Germany"}]},{"given":"Jana M","family":"U'Ren","sequence":"additional","affiliation":[{"name":"School of Plant Sciences, The University of Arizona, Tucson, AZ, USA"}]},{"given":"Georgiana","family":"May","sequence":"additional","affiliation":[{"name":"Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA"}]},{"given":"Fran\u00e7ois","family":"Lutzoni","sequence":"additional","affiliation":[{"name":"Department of Biology, Duke University, Durham, NC, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,12,21]]},"reference":[{"key":"2023020205012760700_btw808-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":"2023020205012760700_btw808-B2","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1080\/15572536.2007.11832578","article-title":"Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR","volume":"99","author":"Arnold","year":"2007","journal-title":"Mycologia"},{"key":"2023020205012760700_btw808-B3","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1093\/sysbio\/syp001","article-title":"A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification?","volume":"58","author":"Arnold","year":"2009","journal-title":"Syst. Biol"},{"key":"2023020205012760700_btw808-B4","doi-asserted-by":"crossref","first-page":"5756","DOI":"10.1073\/pnas.1420815112","article-title":"Continental-scale distributions of dust-associated bacteria and fungi","volume":"112","author":"Barber\u00e1n","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023020205012760700_btw808-B5","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":"2023020205012760700_btw808-B6","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":"2023020205012760700_btw808-B7","doi-asserted-by":"crossref","first-page":"426","DOI":"10.3732\/ajb.1000298","article-title":"The fungi: 1, 2, 3 \u2026 5.1 million species?","volume":"98","author":"Blackwell","year":"2011","journal-title":"Am. J. Bot"},{"key":"2023020205012760700_btw808-B8","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Gutierrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020205012760700_btw808-B9","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"2023020205012760700_btw808-B10","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.ympev.2015.01.008","article-title":"Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order \u2013 Phaeomoniellales","volume":"85","author":"Chen","year":"2015","journal-title":"Mol. Phylogenet. Evol"},{"key":"2023020205012760700_btw808-B11","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1146\/annurev-phyto-080614-120245","article-title":"Identifying and naming plant-pathogenic fungi: past, present, and future","volume":"53","author":"Crous","year":"2015","journal-title":"Annu. Rev. Phytopathol"},{"key":"2023020205012760700_btw808-B12","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":"2023020205012760700_btw808-B13","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1111\/j.1365-294X.1993.tb00005.x","article-title":"ITS primers with enhanced specificity for basidiomycetes\u2013application to the identification of mycorrhizae and rusts","volume":"2","author":"Gardes","year":"1993","journal-title":"Mol. Ecol"},{"key":"2023020205012760700_btw808-B14","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.ympev.2012.01.012","article-title":"Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota)","volume":"63","author":"Gaya","year":"2012","journal-title":"Mol. Phylogenet. Evol"},{"key":"2023020205012760700_btw808-B15","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.funbio.2015.10.002","article-title":"The genome of Xylona heveae provides a window into fungal endophytism","volume":"120","author":"Gazis","year":"2016","journal-title":"Fungal Biol"},{"key":"2023020205012760700_btw808-B16","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/j.ympev.2012.06.019","article-title":"Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes","volume":"65","author":"Gazis","year":"2012","journal-title":"Mol. Phylogenet. Evol"},{"key":"2023020205012760700_btw808-B17","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/S0953-7562(09)80810-1","article-title":"The fungal dimension of biodiversity: magnitude, significance, and conservation","volume":"95","author":"Hawksworth","year":"1991","journal-title":"Mycol. Res"},{"key":"2023020205012760700_btw808-B18","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1017\/S0953756201004725","article-title":"The magnitude of fungal biodiversity: the 1.5 million species estimate revisited","volume":"105","author":"Hawksworth","year":"2001","journal-title":"Mycol. Res"},{"key":"2023020205012760700_btw808-B19","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/j.mycres.2007.03.004","article-title":"A higher-level phylogenetic classification of the Fungi","volume":"111","author":"Hibbett","year":"2007","journal-title":"Mycol. Res"},{"key":"2023020205012760700_btw808-B20","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1038\/nature05110","article-title":"Reconstructing the early evolution of Fungi using a six-gene phylogeny","volume":"443","author":"James","year":"2006","journal-title":"Nature"},{"key":"2023020205012760700_btw808-B21","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1093\/bioinformatics\/btq224","article-title":"Parallelization of the MAFFT multiple sequence alignment program","volume":"26","author":"Katoh","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020205012760700_btw808-B22","doi-asserted-by":"crossref","first-page":"e81718.","DOI":"10.1371\/journal.pone.0081718","article-title":"Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity","volume":"8","author":"Kemler","year":"2013","journal-title":"PLoS One"},{"key":"2023020205012760700_btw808-B23","doi-asserted-by":"crossref","DOI":"10.1079\/9780851998268.0000","volume-title":"Ainsworth & Bisby's Dictionary of the Fungi","author":"Kirk","year":"2008","edition":"10th edn"},{"key":"2023020205012760700_btw808-B24","doi-asserted-by":"crossref","first-page":"5271","DOI":"10.1111\/mec.12481","article-title":"Towards a unified paradigm for sequence-based identification of fungi","volume":"22","author":"Koljalg","year":"2013","journal-title":"Mol. Ecol"},{"key":"2023020205012760700_btw808-B25","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1080\/106351500750049743","article-title":"Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology","volume":"49","author":"Lutzoni","year":"2000","journal-title":"Syst. Biol"},{"key":"2023020205012760700_btw808-B26","author":"Maddison","year":"2011"},{"key":"2023020205012760700_btw808-B27","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1007\/s00248-014-0563-6","article-title":"Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts","volume":"70","author":"Massimo","year":"2015","journal-title":"Microb. Ecol"},{"key":"2023020205012760700_btw808-B28","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":"2023020205012760700_btw808-B29","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1007\/s00300-002-0449-9","article-title":"A predatory fungus (Hyphomycetes: Lecophagus) attacking Rotifera and Tardigrada in maritime Antarctic lakes","volume":"26","author":"McInnes","year":"2003","journal-title":"Polar Biol"},{"key":"2023020205012760700_btw808-B30","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1080\/15572536.2006.11832636","article-title":"New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes","volume":"98","author":"Miadlikowska","year":"2006","journal-title":"Mycologia"},{"key":"2023020205012760700_btw808-B31","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.ympev.2014.04.003","article-title":"A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families","volume":"79","author":"Miadlikowska","year":"2014","journal-title":"Mol. Phylogenet. Evol"},{"key":"2023020205012760700_btw808-B32","doi-asserted-by":"crossref","first-page":"43","DOI":"10.4137\/EBO.S21501","article-title":"A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway","volume":"11","author":"Miller","year":"2015","journal-title":"Evol. Bioinform. Online"},{"key":"2023020205012760700_btw808-B33","doi-asserted-by":"crossref","first-page":"5544","DOI":"10.1128\/AEM.71.9.5544-5550.2005","article-title":"Fungal community analysis by large-scale sequencing of environmental samples","volume":"71","author":"O'Brien","year":"2005","journal-title":"Appl. Environ. Microbiol"},{"key":"2023020205012760700_btw808-B34","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.soilbio.2013.05.014","article-title":"Illumina metabarcoding of a soil fungal community","volume":"65","author":"Schmidt","year":"2013","journal-title":"Soil Biol. Biochem"},{"key":"2023020205012760700_btw808-B35","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1093\/sysbio\/syp020","article-title":"The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits","volume":"58","author":"Schoch","year":"2009","journal-title":"Syst. Biol"},{"key":"2023020205012760700_btw808-B36","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1080\/15572536.2006.11832630","article-title":"A five-gene phylogeny of Pezizomycotina","volume":"98","author":"Spatafora","year":"2006","journal-title":"Mycologia"},{"key":"2023020205012760700_btw808-B37","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020205012760700_btw808-B38","doi-asserted-by":"crossref","first-page":"1256688.","DOI":"10.1126\/science.1256688","article-title":"Fungal biogeography. Global diversity and geography of soil fungi","volume":"346","author":"Tedersoo","year":"2014","journal-title":"Science"},{"key":"2023020205012760700_btw808-B39","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.mycres.2008.11.015","article-title":"Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples","volume":"113","author":"U'Ren","year":"2009","journal-title":"Mycol. Res"},{"key":"2023020205012760700_btw808-B40","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1007\/s00248-010-9698-2","article-title":"Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens","volume":"60","author":"U'Ren","year":"2010","journal-title":"Microb. Ecol"},{"key":"2023020205012760700_btw808-B41","doi-asserted-by":"crossref","first-page":"898","DOI":"10.3732\/ajb.1100459","article-title":"Host and geographic structure of endophytic and endolichenic fungi at a continental scale","volume":"99","author":"U'Ren","year":"2012","journal-title":"Am. J. Bot"},{"key":"2023020205012760700_btw808-B42","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.ympev.2016.02.010","article-title":"Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota)","volume":"98","author":"U'Ren","year":"2016","journal-title":"Mol. Phylogenet. Evol"},{"key":"2023020205012760700_btw808-B43","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1111\/1755-0998.12252","article-title":"Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi","volume":"14","author":"U'Ren","year":"2014","journal-title":"Mol. Ecol. Resour"},{"key":"2023020205012760700_btw808-B44","doi-asserted-by":"crossref","first-page":"4238","DOI":"10.1128\/jb.172.8.4238-4246.1990","article-title":"Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species","volume":"172","author":"Vilgalys","year":"1990","journal-title":"J. Bacteriol"},{"key":"2023020205012760700_btw808-B45","first-page":"315","volume-title":"PCR Protocols: A Guide to Methods and Applications","author":"White","year":"1990"},{"key":"2023020205012760700_btw808-B46","doi-asserted-by":"crossref","first-page":"13022","DOI":"10.1073\/pnas.1209872109","article-title":"Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape","volume":"109","author":"Zimmerman","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/8\/1160\/49038776\/bioinformatics_33_8_1160.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/8\/1160\/49038776\/bioinformatics_33_8_1160.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T06:57:46Z","timestamp":1718953066000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/8\/1160\/2730230"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,12,21]]},"references-count":46,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2017,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw808","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,4,15]]},"published":{"date-parts":[[2016,12,21]]}}}