The Cluster Picker identifies clusters in newick-formatted trees containing thousands of sequences within a few minutes. Cut-offs for within cluster genetic distance and bootstrap support are selected by the user.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install cluster-picker
and update with:
conda update cluster-picker
A Docker container is available at https://quay.io/repository/biocontainers/cluster-picker.