The cluster_aggd command performs
agglomerative clustering of a distance matrix in
tabbed pairs format. To cluster sequences, use
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.
usearch -cluster_aggd mx.txt -treeout tree.phy -clusterout clusters.txt -id 0.80 -linkage min