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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mothur article

mothur citations

 (5)
2017
PMCID: 5607297

[…] with qiime47. the split_libraries_fastq.py was used to de-multiplex the fastq-formatted sequences, and sequences were screened for a phred quality score of 20. trimmed sequences were analyzed using mothur v 1.34.048. sequences were aligned against the silva v 123 seed alignment (silva.seed_v123.tgz) provided on the mothur website (http://mothur.org/wiki/silva_reference_files). the alignment […]

2016
PMCID: 4969246

[…] for rarefaction analysis. pacific biosciences reads were parsed so that quality scores of zero were interpreted as corresponding to an ambiguous base call, and then filtered for quality (≥q30) using mothur. sequences that contained read lengths shorter than 1200 bp were removed. read directionality was checked and corrected where necessary. for all reads, homopolymers >7 were discarded […]

2016
PMCID: 4852915

[…] chimeric sequences. sequencing noise was further reduced using a preclustering methodology [20]. clean and high-quality sequences were then assigned to bacteria and archaea by the cluster command in mothur. downstream analysis for operational taxonomic units (otus) classification, alpha, and beta diversities were done separately for archaea and bacteria. a 97% similarity cutoff was used […]

2016
PMCID: 4824760

[…] 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 […]

2013
PMCID: 3892781

[…] platform at the baylor college of medicine human genome sequencing center as described elsewhere (http://www.mothur.org/wiki/454_sop). we curated our sequences as described previously using the mothur software package (35–37). briefly, we denoised sequences using the pyronoise algorithm after trimming each flowgram to 450 flows (38), aligned the resulting sequences to a reference alignment […]

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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