Phylogenetic tree for 2000 genomes

I want to build a phylogenetic tree for ~2000 genomes with high diversity.
I followed the tutorial but not sure what is the best way to do that with phylphlan 3.1.22.
Based on the different examples, it seems that the tree of life is the most relevant one, so instead of downloading the genomes of TOL I put all of my 2000 genomes in the input dir.
I have the following questions:

  1. Is that the right way to do it?
  2. What are the steps to build the tree? I can see that config file set amino acid as the database, why? the input is genomes
  3. The run time takes very long (mapping ~100 genomes took 2 days) and idea how to speed things up?
    4.If I want to build it based on nucelic acids how should I update the confing?

This is how the config was built:
phylophlan_write_config_file -d a -o tol_similar.cfg --db_aa diamond --map_dna diamond --map_aa diamond --msa mafft --trim trimal --tree1 iqtree --verbose