Clearcut protocols

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Clearcut specifications


Unique identifier OMICS_15083
Name Clearcut
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Aligned sequences
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages C
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.0.9
Stability Stable
Maintained Yes



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  • person_outline Luke Sheneman <>

Publication for Clearcut

Clearcut in pipelines

PMCID: 5792453
PMID: 29386588
DOI: 10.1038/s41598-018-19860-7

[…] based on otu richness (jaccard) or abundance (thetayc). phylotype diversity was determined using ‘phylo.diversity’ script after a phylogenetic tree was constructed for representative otus using ‘clearcut’ script within mothur. the generated phylogeny inference package-formatted distance matrix, based on jaccard and thetayc values, was used for pcoa and nmds to determine microbial community […]

PMCID: 5209367
PMID: 28101080
DOI: 10.3389/fmicb.2016.02064

[…] organic) and among shts within farming system (that is, sht within conventional and organic). the tree was constructed using a distance matrix with relaxed neighbor joining (rnj) algorithm with the clearcut command () available in mothur and displayed using itol ()., microbial communities were assessed by sequencing the 16s rrna gene partial fragment from a short-term experiment with different […]

PMCID: 4709690
PMID: 26754178
DOI: 10.1038/srep19189

[…] between mice grouped by cftr genotype and treatment, were determined by fisher’s exact test in graphpad prism v5.03., with the microbiome sequence dataset, phylogenetic trees were constructed using clearcut via mothur. to investigate the compositional similarity between samples, bray-curtis dissimilarities were calculated for each model and were visualized using two dimensional non-metric […]

PMCID: 4914511
PMID: 27446017
DOI: 10.3389/fmicb.2016.00976

[…] in mothur, to assess the similarity between communities membership (unifrac.unweighted command) and structure (unifrac.weighted command). relaxed neighbor joining phylogenetic tree was done using clearcut () implemented in mothur, and visualized through itol ()., water temperatures measured at midday were 15.3 and 11.3°c in e72-red and e73-green ponds, respectively, whereas in the lagoon […]

PMCID: 4696820
PMID: 26716685
DOI: 10.1371/journal.pone.0144804

[…] and were subsampled to 2,000 sequences per sample, giving 20,000 per group per time point. this subsample was used to create a neighbor-joining tree using the mothur-integrated algorithms for clearcut [], linear discriminant analysis (lda) using the mothur-integrated lefse [], and principal coordinate analysis (pcoa) []., real-time pcr was used to calculate archaeal and protozoal […]

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Clearcut in publications

PMCID: 5938447
PMID: 29760910
DOI: 10.1002/ece3.3977

[…] were used to estimate the beta diversity and visualized with pcoa. bray–curtis distance metric was performed on relative sequence abundances after square root transformation. commands in mothur (clearcut, unifrac.unweighted, and unifrac.weighted) were used for unifrac distance metrics. permanova using the vegan package in r was used to determine the significance of clustering in the pcoa […]

PMCID: 5874073
PMID: 29590198
DOI: 10.1371/journal.pone.0195112

[…] []). kruskal-wallis tests were performed as described above to determine significance between inverse simpson of different samples., the verrucomicrobia phylogenetic tree was created in mothur using clearcut (relaxed neighbor joining algorithm) using uncorrected pairwise distance between aligned sequences (dist.seqs)) after extracting representative sequences for 1,323 otus using get.oturep. […]

PMCID: 5835928
PMID: 29541023
DOI: 10.3389/fnbeh.2018.00031

[…] morally right to opt for self-preservation, which may be supported by moral egoism. although it is debated whether this is an ethical theory proper., on the deontological side the demands aren't as clearcut. thomson herself is not sure what exactly deontology would prescribe and ultimately leaves the question open (thomson, , p. 371). nevertheless, if we consider human behavior to get […]

PMCID: 5825053
PMID: 29474487
DOI: 10.1371/journal.pone.0193132

[…] regnans) ecosystem in the central highlands of victoria, south-eastern australia. this ecosystem has been subject to extensive and intensive wildfires in the past decade [], and to widespread clearcut logging [,]. there are also landscapes where there has been limited or no logging or fire, making the mountain ash ecosystem a valuable one in which to quantify the associations […]

PMCID: 5823377
PMID: 29470534
DOI: 10.1371/journal.pone.0192770

[…] underwent “isohydric dialysis” for 90 minutes and then were switched to standard buffer (bicarbonate = 37mmol/l). a second dialysis, 2 days later, employed standard buffer throughout., we found a clearcut separation of blood ph and bicarbonate concentrations after 90 minutes of “isohydric dialysis” (ph = 7.37, bicarbonate = 22.4 mmol/l) and standard dialysis (ph = 7.49, bicarbonate = 29.0 […]

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Clearcut institution(s)
Department of Biological Sciences, University of Idaho, Moscow, ID, USA
Clearcut funding source(s)
This project was funded by NIH P20 RR16454 from the INBRE Program of the National Center for Research Resources and by NIH NCRR 1P20 RR16448.

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