mothur protocols

mothur specifications

Information


Unique identifier OMICS_01518
Name mothur
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.38.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Mothur

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Publication for mothur

mothur IN pipelines

 (11)
2017
PMCID: 5281551
PMID: 28197133
DOI: 10.3389/fmicb.2017.00067

[…] used for further analysis., 16s (2,421,511 reads) and 18s rrna (945,524 reads) sequences from the total rna sample were used to assess rumen prokaryotic and eukaryotic diversity, respectively, using mothur (rrid:scr_011947; schloss et al., 2009) following the analysis pipeline used by li et al. (2016), except that the silva database was used as reference database. briefly, the v1-v3 region […]

2017
PMCID: 5510586
PMID: 28717593
DOI: 10.7717/peerj.3529

[…] (he et al., 2016). furthermore, as an approximate measure for the number of lactobacillus otus recovered with our approach, we used the average neighbor clustering algorithm as implemented in mothur version 1.34.4 (schloss et al., 2009)., although our aim was not to recover all, but only the highly covered symbiont data from honey bee short reads, we wanted to test if our screening […]

2016
PMCID: 4824760
PMID: 27092104
DOI: 10.3389/fmicb.2016.00372

[…] the sequencing data has been deposited at the national centre for biotechnology information under bioproject accession no. prjna297134., 16s rrna gene sequencing data was processed using the mothur pipeline (kozich et al., 2013). sequence reads were discarded on a per-contig basis, if sequences contained an n base or had more than eight homopolymers. trimmed sequences were aligned using […]

2016
PMCID: 4870698
PMID: 27188959
DOI: 10.1038/srep26276

[…] clustered into different taxon ranks according to the consensus taxonomy of the unique tags (representative of each otu)., richness and biodiversity indices for the otus were calculated using the mothur software package22, with its implementation of chao1 and the non-parametric shannon42 formula. richness was estimated using the chao1 index, whereas diversity, which depends on how uniformly […]

2016
PMCID: 4870698
PMID: 27188959
DOI: 10.1038/srep26276

[…] on how uniformly the sequences are spread across different otus, was estimated using the non-parametric shannon formula. rarefaction curves were calculated and plotted with a combination of the mothur22 and r statistical software packages. a principal coordinate analysis (pcoa) at the genus level according to bray-curtis dissimilarities was carried out using qiime43. pearson’s correlations […]

mothur institution(s)
Department of Microbiology, University of Massachusetts, Amherst, MA, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA; Department of Biology, University of New Mexico, Albuquerque, NM, USA; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA; Department of Biological Sciences, University of Warwick, Coventry, UK; Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada; Environmental Science and Engineering, Colorado School of Mines, Golden, CO; Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia; Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
mothur funding source(s)
Funding for mothur has been provided by the College of Natural Resources and the Environment at the University of Massachusetts, a grant from the Sloan Foundation, a grant from the National Science Foundation (award 0743432), and the Austrian GEN-AU project BIN.

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