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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 citations


The influence of diet and environment on the gut microbial community of field crickets

Ecol Evol
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 […]


Verrucomicrobia are prevalent in north temperate freshwater lakes and display class level preferences between lake habitats

PLoS One
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. […]


Autonomous Vehicles Require Socio Political Acceptance—An Empirical and Philosophical Perspective on the Problem of Moral Decision Making

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 […]


Empirical relationships between tree fall and landscape level amounts of logging and fire

PLoS One
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 […]


The effect of isohydric hemodialysis on the binding and removal of uremic retention solutes

PLoS One
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 […]


Cell Behaviors during Closure of the Choroid Fissure in the Developing Eye

PMCID: 5826230
PMID: 29515375
DOI: 10.3389/fncel.2018.00042

[…] neural-crest derived pom can lead to optic vesicle morphogenesis defects and coloboma (bazin-lopez et al., ). however, conclusions on the role of neural crest pom in early eye development are not clearcut; indeed loss of function of some genes impacting neural crest derived-pom, such as foxc1 in mouse, does not appear to lead to coloboma and foxc1 mutations in humans are only rarely […]

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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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