Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities-Reference-Cited by-同舟云学术

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

Published:2009-12 Issue:23 Volume:75 Page:7537-7541
ISSN:0099-2240
Container-title:Applied and Environmental Microbiology
language:en
Short-container-title:Appl Environ Microbiol

Author:

Schloss Patrick D.¹²,Westcott Sarah L.¹²,Ryabin Thomas¹,Hall Justine R.³,Hartmann Martin⁴,Hollister Emily B.⁵,Lesniewski Ryan A.⁶,Oakley Brian B.⁷,Parks Donovan H.⁸,Robinson Courtney J.²,Sahl Jason W.⁹,Stres Blaz¹⁰,Thallinger Gerhard G.¹¹,Van Horn David J.²,Weber Carolyn F.¹²

Affiliation:

1. Department of Microbiology, University of Massachusetts, Amherst, Massachusetts

2. Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan

3. Department of Biology, University of New Mexico, Albuquerque, New Mexico

4. Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada

5. Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas

6. Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota

7. Department of Biological Sciences, University of Warwick, Coventry, United Kingdom

8. Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada

9. Environmental Science and Engineering, Colorado School of Mines, Golden, Colorado

10. Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia

11. Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria

12. Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana

Abstract

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.

Publisher

American Society for Microbiology

Subject

Ecology,Applied Microbiology and Biotechnology,Food Science,Biotechnology

Link

https://journals.asm.org/doi/pdf/10.1128/AEM.01541-09

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