clearcut
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 https://github.com/ibest/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
Known Issues:
Sequence names
Sequence names must include non-numeric characters. If your sequence names contain only numeric characters you will see the following error message, “Clearcut: Syntax error in distance matrix at offset xxx.” The message is produced because clearcut misinterprets your sequence names as distances in the matrix and assumes a corrupted file at location xxx (the first sequence name). To resolve this issue you can rename your sequences to include non numeric characters. You can do this with the rename.seqs command as follows:
mothur > rename.seqs(fasta=current, count=current, delim=”_”)
The above command will create sequence names like: number_sampleName. A sequence like 8890009098890 belonging to sample1 would become 1_sample1. The rename.seqs command creates a map file you can use to restore the original names if desired.
mothur > rename.seqs(fasta=current, map=mapFileCreatedByFirstRenameSeqsCommand)
Revisions
- 1.28.0 Bug Fix - windows crash
- 1.48.0 Fixes crash with clearcut sequence name copy