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cluster_aggd command
Commands > Clustering

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 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.


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