The tree2clusters command creates from a tree in Newick format, which must have branch lengths specified. Branch lengths must be specified as 1.0 – (fractional sequence identity).
Clusters are created based on an identity cutoff, which is specified by the -id option.
Output is to a tabbed text file specified by the -clusterout option. Fields are cluster_number and label.
Example
usearch -tree2clusters tree,phy -id 0.95 -clusterout
clusters.txt