Marker genes and missin/over-represented genes

[Adi Lavy]

I have some questions I could not find an answer to in regards to how PhyloPhlAn operates. I was hoping I might find someone who may be able to provide some answers:

1. Where can I find a list of the marker genes that PhyloPhlAn uses? and are these updated to support the identification of Candidate Phyla Radiation (CPR) bacteria and DPANN?

2. How does PhyloPhlAn deal with missing / split / multiple copies of marker genes that often occur in genomes from metagenomes?

Thanks !!!

Adi