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 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.


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

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



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


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


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

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


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

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


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

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


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

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


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

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


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

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


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

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


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

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


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)


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)


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

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


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


  • 1.28.0 Bug Fix - windows crash
  • 1.48.0 Fixes crash with clearcut sequence name copy