Hi,
indeed there was one more script by the time we submitted the paper. It was called panphlan_find_gene_grp.py. You can actually find it in the 3.0.1 release of PanPhlAn here.
We actually removed it in the latest release for it was still very experimental and changed a lot. We are currently working on improving and expending these functionalities in a new release and the code still need some work.
This script (the old version in PanPhlAn 3.0.1) will perform clustering of genes families based on co-presence/absence.
It can also provide a basic Heatmap visualization of the PanPhlAn profile. If you are more interested in the visualization part, check also Tutorial; guidance on vizualisation - #2 by leonard.dubois
Let me know if you have any question regarding this script.
Best regards
Leonard