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Cluster.split (version 1.39.5.0)

Split by:

VSEARCH methods (agc and dgc) require a fasta file

Select a Distance Matrix Format:

column - Distance Matrix:

name file or count table - Sequences Name reference:

Clustering Method:

metric - select the metric in the opticluster method:

Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn), false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score), accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.

Initial randomization:

singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu

set the stable value for the metric in the opticluster method:

The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0.

Maximum number of iterations:

cutoff - Distance Cutoff threshold - ignored if not > 0:

Ignore pairwise distances larger than this, a common value would be 0.25

precision - Precision for rounding distance values:

Set higher precision for longer genome scale sequence lengths

large - distance matrix is too large to fit in RAM:

If your job fails due to not enough memory error, set this to true to rerun

perform clustering?:

indicate whether you want to run the clustering or just split the distance matrix

runsensspec:

run the sens.spec command on the completed list file

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The cluster.split command assign sequences to OTUs (Operational Taxonomy Unit).

v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean.