The cluster_aggd command performs agglomerative clustering of a distance matrix in tabbed pairs format. To cluster sequences, use cluster_agg.
The calc_distmx command can be used to calculate a distance matrix.
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 tree.phy -clusterout clusters.txt -id 0.80 -linkage min