UCLUST statistics

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Citations per year

Number of citations per year for the bioinformatics software tool UCLUST

Tool usage distribution map

This map represents all the scientific publications referring to UCLUST per scientific context
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UCLUST specifications


Unique identifier OMICS_01448
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for UCLUST

UCLUST citations


Diversity and antimicrobial potential in sea anemone and holothurian microbiomes

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

[…] efault parameters were used, with a minimun Phred quality score <20 and ambiguous nucleotides were removed. Sequence alignment was made using Greengenes database [] and PyNast alignment algorithm []. UCLUST software [] was used to assign similar sequences to operational taxonomic units (OTUs) by clustering sequences based on a 97% similarity threshold. The taxonomic assignment was achieved in diff […]


What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

PMCID: 5956146
PMID: 29743201
DOI: 10.1128/mSphere.00122-18
call_split See protocol

[…] pick_open_reference_otus.py script using the USEARCH algorithm v6.1544 against the SILVA reference data set version 128 (). Representative sequences for each OTU were taxonomically assigned using the UCLUST-based consensus classifier with default settings (). OTUs that were classified to the Archaea phylum were filtered from the OTU table and normalized to 1,000 sequences per sample. α and β diver […]


Near full length 16S rRNA gene next generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae

PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…]  nt) were analyzed with QIIME 1.9.1 [] using the Oracle VM VirtualBox version 5.0.26 r108824. Operational taxonomic units (OTUs) were picked using the two-step open-reference picking method using the UCLUST algorithm [], as implemented in QIIME using the pick_open_reference_otus.py command. Default settings were used, with the exception of picking OTUs at 99% similarity and training the RDP classi […]


Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare

Sci Rep
PMCID: 5934373
PMID: 29725059
DOI: 10.1038/s41598-018-25450-4

[…] iconNoise, and chimeras were removed using Perseus. All reads shorter than 250 bp were discarded and the remaining reads were clustered into Operational Taxonomic Units (OTUs) at 97% similarity using uclust. Representative sequences were aligned against the Silva reference alignment (release 108,) using PyNAST and identified using the RDP Classifier. Rare OTUs (i.e. singletons and doubletons) were […]


High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

Front Microbiol
PMCID: 5943533
PMID: 29774020
DOI: 10.3389/fmicb.2018.00887

[…] TU assignment, alpha diversity, and beta diversity calculations, were subsequently completed using the QIIME software package (). OTUs were defined at the identity levels of 80, 90, 95, and 97% using UCLUST () based on nucleotide sequences. The first sequence within each OTU cluster was picked as a representative sequence. The representative sequences were aligned with MUSCLE and used to construct […]


Killing Effects of an Isolated Serratia marcescens KH 001 on Diaphorina citri via Lowering the Endosymbiont Numbers

Front Microbiol
PMCID: 5938409
PMID: 29765368
DOI: 10.3389/fmicb.2018.00860
call_split See protocol

[…] mplemented for Bioinformatics analysis (). Briefly, 16S rRNA operational taxonomic units (OTUs) were clustered using an open-reference OTU picking protocol based on 97% nucleotide similarity with the UCLUST algorithm (), and ChimeraSlayer was applied to remove chimeric sequences (). The relative abundance of each OTU was determined as a proportion of the sum of sequences for every sample, taxonomi […]

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UCLUST institution(s)
Tiburon, CA, USA

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