Recommended approach for building phylogenetic tree from de novo metagenomes

I have about 650 metagenome assembled genomes (MAG) that cluster into about 150 unique species level designations from FastANI. For each of the clusters, I have a nearest reference.

I want to create a phylogenetic tree of these MAGs. I had a few questions:

1. Is it expected for a high-level publication that a nearest reference is included for each species level cluster? Or is it standard to just make the phylogenetic tree with my MAGs and then put in a table somewhere what the nearest references are?

2. Is it accepted to create a phylogenetic tree from FastANI values or does this go against the norm since it isn’t based on proteins?

3. I have both bacterial and viral MAGs. I would do concatenated protein alignments for the bacteria, but how would you do it for viruses since they don’t really have conserved marker genes?