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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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Documentation


Publication for mothur

mothur citations

 (2260)
library_books

Different clusters of Candidatus ‘Methanoperedens nitroreducens’ like archaea as revealed by high throughput sequencing with new primers

2018
Sci Rep
PMCID: 5955947
PMID: 29769540
DOI: 10.1038/s41598-018-24974-z

[…] -3′):TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATCTGGCTCGGYGGCTACATGT.Modified McrA 1360 R primer (5′-3′):GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTGCCTCTTTGTGGAGGTACATGGA.The sequencing data were analysed using the Mothur (version 1.33.2) according to the standard operating procedure,. Briefly, the sequences were sorted into different samples by matching the specific barcodes. Then, the primers, barcodes, adapto […]

library_books

High species diversity of trichostrongyle parasite communities within and between Western Canadian commercial and conservation bison herds revealed by nemabiome metabarcoding

2018
PMCID: 5952520
PMID: 29764472
DOI: 10.1186/s13071-018-2880-y

[…] Beta diversity, at the population level, among provinces and conservation herds was assessed with the weighted UniFrac function in Mothur, which revealed marked differences in the species present between populations (where a score of 0 indicates that populations are identical and a score of 1 indicates they are completely differe […]

call_split

The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens

2018
Microbiome
PMCID: 5948730
PMID: 29753324
DOI: 10.1186/s40168-018-0477-5
call_split See protocol

[…] 380214 under the SRA study SRP133552.Prior to metagenomic analysis, sequence reads with a quality score mean below 30 were removed using Prinseq []. The 16S rRNA sequence analysis was performed using Mothur v. 1.39 []. Analysis was performed as according to the MiSeq SOP (accessed online 28/06/2017; []). The 16S rRNA gene sequences were aligned against a reference alignment based on the SILVA rRNA […]

library_books

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes

2018
PLoS One
PMCID: 5942802
PMID: 29742123
DOI: 10.1371/journal.pone.0196178

[…] s of 250 bp. For data analysis, the forward and reverse fastq files were concatenated, filtered by read quality (Phred Score) and the barcodes and primers sequences were eliminated using QIIME [] and MOTHUR []. The final length of V4 sequences was ∼252 bp. For quality filtering, QIIME default parameters were used, with a minimun Phred quality score <20 and ambiguous nucleotides were removed. Seque […]

call_split

Research on oral microbiota of monozygotic twins with discordant caries experience in vitro and in vivo study

2018
Sci Rep
PMCID: 5940813
PMID: 29740156
DOI: 10.1038/s41598-018-25636-w
call_split See protocol

[…] ral Microbiome Database with confidence threshold of 70%. Alpha diversity indices (Shannon index, Simpson index) and richness estimators (ACE index and Chao 1 index) calculations were performed using Mothur v.1.30.2. Phylogenetic beta diversity measures such as the unweighted UniFrac distance metrics analysis was determined using the represent sequences of OTUs for each sample, and principal compo […]

call_split

The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses

2018
PMCID: 5936483
PMID: 29730829
DOI: 10.1186/s13568-018-0607-2
call_split See protocol

[…] Sequences from both runs were merged resulting in a total of 216,660 reads with an average length of 252 nucleotides. The reads were analysed using Mothur (v1.38; Schloss et al. ) and the Mothur 454 SOP (Schloss et al. ). First, reads were quality filtered on read length (200–450 bp) allowing for homopolymers (maximum 8), a maximum of 2 differenc […]

Citations

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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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