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Cluster (version
generated by count.seqs
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.
singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu
The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0.
Ignore pairwise distances larger than this, a common value would be 0.10
Set higher precision for longer genome scale sequence lengths

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 command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix or a column-formatted_distance_matrix and name file. It generates a list, a sabund (Species Abundance), and a rabund (Relative Abundance) file.