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Clearcut

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The clearcut command allows mothur users to run the clearcut program from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/ Note: In version 1.13.0 the clearcut source was added to mothur, so you no longer need the clearcut executable. You can still download the clearcut executable if you would like, Download Clearcut.

Default settings

You must provide either an aligned fasta file or a phylip formatted distance matrix. If you provide a fasta file, you must specify DNA or protein.

mothur > clearcut(phylip=abrecovery.dist)

Note: clearcut requires sequence names to be at least 10 characters long.

or

mothur > clearcut(fasta=abrecovery.align, DNA=T)

In both cases clearcut will generate a file called abrecovery.tre.

Options

version

The version parameter prints out the version of clearcut you are using, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=T, version=t)
Clearcut Version: 1.0.9

verbose

The verbose parameter prints out more output from clearcut, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=T, verbose=t)
PRNG SEED: 1274107574
Tree is not additive
RNJ tree built in 0.001938 secs
Relaxed NJ tree(s) in abrecovery.tre

quiet

The quiet parameter turns on silent operation mode, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=T, quiet=t)


seed

The seed parameter allows you to explicitly set the PRNG seed to a specific value.

mothur > clearcut(fasta=abrecovery.align, DNA=t, seed=12345)

norandom

The norandom parameter allows you to attempt joins deterministically, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=t, norandom=t)

shuffle

The shuffle parameter allows you to randomly shuffle the distance matrix, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=t, shuffle=t)

neighbor

The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=t, neighbor=t)

stdout

The stdout parameter outputs your tree to STDOUT, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=t, stdout=t)

DNA

The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F.

mothur > clearcut(fasta=abrecovery.align, DNA=t)

protein

The protein parameter allows you to indicate your fasta file contains protein sequences, default=F

mothur > clearcut(fasta=abrecovery.align, protein=t)

matrixout

The matrixout parameter allows you to specify a filename to output a distance matrix to.

 mothur > clearcut(fasta=abrecovery.align, DNA=t, matrixout=myDist.dist)

ntrees

The ntrees parameter allows you to specify the number of output trees you want clearcut to generate, default=1.

 mothur > clearcut(fasta=abrecovery.align, DNA=t, ntrees=5)

expblen

The expblen parameter allows you to use exponential notation for branch lengths, default=F.

 mothur > clearcut(fasta=abrecovery.align, DNA=t, expblen=t)

expdist

The expdist parameter allows you to use exponential notation for distance outputs, default=F.

 mothur > clearcut(fasta=abrecovery.align, DNA=t, expdist=t, matrixout=myDist.dist)


Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: A Fast Distance-Based Phylogenetic Tree Construction Method, J. Mol. Evol., 62, 785-792

Revisions

  • 1.28.0 Bug Fix - windows crash