cluster_aggd command

The cluster_aggd command performs agglomerative clustering of a distance matrix in tabbed pairs format.

The calc_distmx command can be used to calculate a distance matrix for sequences.

The beta_div command can be used to calcualte a distance matrix for samples in an OTU table .

Cluster linkage is specified using the - linkage option , which may be set to max (the default), min or avg.

Output is reported as a tree in Newick format specified by the - treeout option and/or as a clusters file specified by the - clusterout option . If a clusters file is specified, then the - id option must be given to specify the identity threshold.

Example

usearch -cluster_aggd mx.txt -treeout clusters.tree -clusterout clusters.txt \
-id 0.80 -linkage min