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Methods

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D. Schloss, 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
Patrick D. Schloss
1Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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  • For correspondence: pschloss@umich.edu
Sarah L. Westcott
1Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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Thomas Ryabin
1Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
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Justine R. Hall
3Department of Biology, University of New Mexico, Albuquerque, New Mexico
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Martin Hartmann
4Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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Emily B. Hollister
5Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas
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Ryan A. Lesniewski
6Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota
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Brian B. Oakley
7Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
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Donovan H. Parks
8Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
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Courtney J. Robinson
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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Jason W. Sahl
9Environmental Science and Engineering, Colorado School of Mines, Golden, Colorado
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Blaz Stres
10Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
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Gerhard G. Thallinger
11Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
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David J. Van Horn
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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Carolyn F. Weber
12Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana
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DOI: 10.1128/AEM.01541-09
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ABSTRACT

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur 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. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

  • Copyright © 2009 American Society for Microbiology
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss, 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
Applied and Environmental Microbiology Nov 2009, 75 (23) 7537-7541; DOI: 10.1128/AEM.01541-09

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss, 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
Applied and Environmental Microbiology Nov 2009, 75 (23) 7537-7541; DOI: 10.1128/AEM.01541-09
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  • Top
  • Article
    • ABSTRACT
    • Introducing mothur.
    • Object oriented, responsive, free, and platform independent.
    • Open documentation and support.
    • Example workflow: the ocean's rare biosphere.
    • Looking forward.
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

biodiversity
Computational Biology
metagenomics
Software

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