PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

Keywords

Workbench, Metadata, Annotation, Computer science, Terminology

References

• Proposal to 'Wikify' GenBank Meets Stiff ResistanceElizabeth Pennisi — 2008
• A constructive step towards selecting a DNA barcode for fungi.Ursula Eberhardt — 2010
• An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants. APG IIIApg Iii — 2009
• Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species IdentificationR. Henrik Nilsson, Erik Kristiansson, Martin Ryberg — 2008
• Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungiR. Henrik Nilsson, Erik Kristiansson, Martin Ryberg — 2005
• An open source chimera checker for the fungal ITS regionR. Henrik Nilsson, Kessy Abarenkov, Vilmar Veldre — 2010
• The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA SequencingLes Dethlefsen, S. M. Huse, Mitchell L. Sogin — 2008
• Rethinking taxon sampling in the light of environmental sequencingR. Henrik Nilsson, Martin Ryberg, Elisabet Sjökvist — 2011
• Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARBTodd Z. DeSantis, Philip Hugenholtz, N. Larsen — 2006
• Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distributionJens Reeder, Rob Knight — 2010
• Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)Martin Ryberg, R. Henrik Nilsson, Erik Kristiansson — 2008
• Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead.Konstantinos T. Konstantinidis, James M. Tiedje — 2007
• Accurate determination of microbial diversity from 454 pyrosequencing dataChristopher Quince, Anders Lanzén, Thomas P. Curtis — 2009
• Global patterns in bacterial diversityCatherine Lozupone, Rob Knight — 2007
• Microbiological Common Language (MCL): a standard for electronic information exchange in the Microbial Commons.Bert Verslyppe, Renzo Kottmann, Wim De Smet — 2010
• A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientationR. Henrik Nilsson, Vilmar Veldre, Zheng Wang — 2011
• A plea for DNA taxonomyDiethard Tautz, Peter Arctander, Alessandro Minelli — 2003
• A modern approach to rotiferan phylogeny: combining morphological and molecular data.Martin V. Sørensen, Gonzalo Giribet — 2006
• Current state and perspectives of fungal DNA barcoding and rapid identification proceduresDominik Begerow, R. Henrik Nilsson, Martin Unterseher — 2010
• The UNITE database for molecular identification of fungi--recent updates and future perspectives.Kessy Abarenkov, R. Henrik Nilsson, Karl‐Henrik Larsson — 2010

Cited by

• Methods for DNA barcoding of fungi.Ursula Eberhardt — 2012
• Strepsiptera species in Estonia.Villu Soon, Tonu. Keskula, Olavi Kurina — 2012
• Metagenomic data of fungal internal transcribed Spacer and 18S rRNA gene sequences from Lonar lake sediment, IndiaPravin Dudhagara, Anjana Ghelani, Sunil Bhavsar — 2015
• FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guildNhu Nguyen, Zewei Song, Scott T. Bates — 2016
• Impact of metal pollution on fungal diversity and community structures.Michiel Op De Beeck, Bart Lievens, Pieter Busschaert — 2015
• Tree diversity and species identity effects on soil fungi, protists and animals are context dependentLeho Tedersoo, Mohammad Bahram, Tomáš Cajthaml — 2015
• Characterisation of diverse microbial communities and application of novel detection techniquesKaisa Koskinen — 2013
• Fungal High‐throughput Taxonomic Identification tool for use with Next‐Generation Sequencing (FHiTINGS)Karen C. Dannemiller, Darryl Reeves, Kyle Bibby — 2014
• Type studies on Coprinus dunarum StollIrja Saar, Kuulo Kalamees, Edgars Vimba — 2015
• Peremeestaime, veerežiimi ja mullaomaduste mõju pajuliste ektomükoriisaleMarit Mett — 2013
• PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platformHyun S. Gweon, Anna Oliver, Joanne E. Taylor — 2015
• Standardizing metadata and taxonomic identification in metabarcoding studiesLeho Tedersoo, Kelly S. Ramirez, R. Henrik Nilsson — 2015
• Towards global patterns in the diversity and community structure of ectomycorrhizal fungi.Leho Tedersoo, Mohammad Bahram, Märt Toots — 2012
• Phylogeny and mycorrhizal associations of NyctaginaceaeLaura Suur — 2013
• An Illumina metabarcoding pipeline for fungiMiklós Bálint, Philipp‐André Schmidt, Rahul Sharma — 2014
• Revealing Natural Relationships among Arbuscular Mycorrhizal Fungi: Culture Line BEG47 Represents Diversispora epigaea, Not Glomus versiformeArthur Schüßler, Manuela Krüger, Christopher Walker — 2011
• Scuttle Flies (Diptera: Phoridae) Reared from Fungi in BeninR. H. L. Disney, Olavi Kurina, Leho Tedersoo — 2013
• Finding needles in haystacks: linking scientific names, reference specimens and molecular data for FungiConrad L. Schoch, Barbara Robbertse, Vincent Robert — 2014
• ITS1 versus ITS2 as DNA metabarcodes for fungiRakel Blaalid, Surendra Kumar, R. Henrik Nilsson — 2013
• Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences.R. Henrik Nilsson, Leho Tedersoo, Kessy Abarenkov — 2012

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