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Cluster.classic (version 1.39.5.0)

phylip - Distance Matrix:

format must be mothur.lower.dist or mothur.square.dist

name - Sequences Name reference:

count - a count_table:

generated by count.seqs

method - Select a Clustering Method:

cutoff - Distance Cutoff threshold:

Ignore pairwise distances larger than this. Default for methods opti,agc,dgc is 0.03, default for the other methods is 0.15

precision - Precision for rounding distance values:

Set higher precision for longer genome scale sequence lengths

sim - Matrix values are Similary instead of Distance:

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.classic command assign sequences to OTUs (Operational Taxonomy Unit).