We define cluster confidence biologically by the number of cluster-specific mutations we find in the mutation tables produced by the cluster_mutation.py script. To generalize this idea of cluster confidence or support, we added a new pathogen-cluster-mutations command to the pathogen-embed toolkit which replaces the cluster_mutation.py script.
Description
We define cluster confidence biologically by the number of cluster-specific mutations we find in the mutation tables produced by the
cluster_mutation.pyscript. To generalize this idea of cluster confidence or support, we added a newpathogen-cluster-mutationscommand to the pathogen-embed toolkit which replaces thecluster_mutation.pyscript.