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