46. ARB: A Software Environment for Sequence Data
Ralf Westram,Kai Christian Bader,Elmar Prüsse,Yadhu Kumar,Harald Meier,Frank Oliver Glöckner,Frank Oliver Glöckner,Wolfgang Ludwig +7 more
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The article was published on 2011-05-03 and is currently open access. It has received 1004 citations till now. The article focuses on the topics: Software.read more
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Journal ArticleDOI
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
Anna Klindworth,Elmar Pruesse,Timmy Schweer,Jörg Peplies,Christian Quast,Matthias Horn,Frank Oliver Glöckner +6 more
TL;DR: The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.
Journal ArticleDOI
SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes
TL;DR: The SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project was evaluated and was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks.
Journal ArticleDOI
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
Daniel P. R. Herlemann,Matthias Labrenz,Klaus Jürgens,Stefan Bertilsson,Joanna J Waniek,Anders F. Andersson +5 more
TL;DR: This study reports a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes.
Journal ArticleDOI
SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
TL;DR: SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data, is presented, capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.
References
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
TL;DR: Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.
Journal ArticleDOI
ARB: a software environment for sequence data
Wolfgang Ludwig,Oliver Strunk,Ralf Westram,Lothar Richter,Harald Meier,Yadhukumar,Arno Buchner,Tina Lai,Susanne Steppi,Gangolf Jobb,Wolfram Förster,Igor Brettske,Stefan Gerber,Anton W. Ginhart,Oliver Gross,Silke Grumann,Stefan Hermann,Ralf Jost,Andreas König,Thomas Liss,Ralph Lüßmann,Michael May,Björn Nonhoff,Boris Reichel,Robert Strehlow,Alexandros Stamatakis,Norbert Stuckmann,Alexander Vilbig,Michael Lenke,Thomas Ludwig,Arndt Bode,Karl-Heinz Schleifer +31 more
TL;DR: The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface.
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Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more