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Hcluster (version 1.36.1.0)

Select a Distance Matrix Format:

column - Distance Matrix:

name - Names:

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

Ignore pairwise distances larger than this, a common value would be 0.10

hard - Use hard cutoff instead of rounding:

precision - Precision for rounding distance values:

Set higher precision for longer genome scale sequence lengths

method - Select a Clustering Method:

sorted - The input matrix is already sorted:

showabund - Verbose ouput:

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 hcluster_ 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.