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Information


Unique identifier OMICS_14269
Name DOTUR
Alternative name Distance based OTU and Richness determination
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A PHYLIP-generated distance matrix
Input format PHYLIP
Output data Assigns sequences to operational taxonomic units for every distance level that can be used to form OTUs.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Jo Handelsman

Publication for Distance based OTU and Richness determination

DOTUR citations

 (215)
call_split

Dynamics of phosphorus and bacterial phoX genes during the decomposition of Microcystis blooms in a mesocosm

2018
PLoS One
PMCID: 5933731
PMID: 29723219
DOI: 10.1371/journal.pone.0195205
call_split See protocol

[…] E program [], and the generated files in phylip format were analysed for nucleic acid distance using the DNAdist program []. The similarities in the generated files, as analysed, were compared by the Dotur program to acquire coverage (C), Chao 1 richness estimator (Schao), and the Shannon-Wiener index (H’) in those clone libraries []. Here, the phoX sequences with a ≥97% similarity were defined as […]

call_split

Geochemical Influence on Microbial Communities at CO2 Leakage Analog Sites

2017
Front Microbiol
PMCID: 5684959
PMID: 29170659
DOI: 10.3389/fmicb.2017.02203
call_split See protocol

[…] matrices based on alignment of the library sequences to the RDP database were used as input for further analysis with the Distance Based Operational Taxonomic Units (OTUs) and Richness Determination (DOTUR) program (Schloss and Handelsman, ). All clones having a mutual sequence similarity of more than 97% were grouped into OTUs by using DOTUR. Rarefaction curves (number of OTUs detected vs. the nu […]

call_split

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High Throughput Sequencing

2017
Front Microbiol
PMCID: 5651520
PMID: 29093705
DOI: 10.3389/fmicb.2017.02032
call_split See protocol

[…] T program (). Sequences having frameshift errors were removed. Error-free sequences were then translated into conceptual protein sequences. The NifH protein sequences were grouped into OTUs using the DOTUR program with a 0.05 sequence distance cutoff (; , ; ). Samples were rarefied to 12,000 sequences per sample, and singletons were removed. Taxonomic assignment for nifH OTUs was carried out by se […]

call_split

Small scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia oxidising bacteria Nitrosomonas sp. amoA genes and transcripts

2017
Sci Rep
PMCID: 5643298
PMID: 29038459
DOI: 10.1038/s41598-017-13583-x
call_split See protocol

[…] tP. Protein sequence alignments were constructed using Bioedit (version 7.2). amoA gene sequences displaying more than 97% similarity were grouped into a single operational taxonomic unit (OTU) using DOTUR software by the furthest neighbour approach. Distance matrices were calculated using the PROTDIST program in PHYLIP. Phylogenetic trees were created from the distance matrices using the neighbou […]

library_books

Novel arsenic transforming bacteria and the diversity of their arsenic related genes and enzymes arising from arsenic polluted freshwater sediment

2017
Sci Rep
PMCID: 5593903
PMID: 28894204
DOI: 10.1038/s41598-017-11548-8

[…] on).The sequences were aligned in MEGA 6.0 using the ClustalW tool with its default settings and were manually edited. The OTUs from the arsC, arrA, and aioA gene clone libraries were identified with DOTUR software using an identity cutoff of 97%. The Good’s libraries coverage were calculated using the equation C = 1 − (n/N) × 100, where n is the number of unique OTUs and N is the number of sequen […]

library_books

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

2017
Front Microbiol
PMCID: 5591341
PMID: 28928718
DOI: 10.3389/fmicb.2017.01561

[…] inal similarity cutoff is applied, a fact that is often glossed over when discussing microbiomics.Hierarchical clustering was first made widely available to the ecology community through the software DOTUR (Schloss and Handelsman, ), but can now be found in many implementations, most prominently its successor MOTHUR (Schloss et al., ) and the CD-HIT package (Fu et al., ). As for heuristic strategi […]

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DOTUR institution(s)
Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI, USA
DOTUR funding source(s)
This work was supported by a USDA postdoctoral fellowship in Soil Biology, the NSF Microbial Observatory program (MCB-0132085), the Howard Hughes Medical Institute, and the University of Wisconsin—Madison College of Agricultural and Life Sciences.

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