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:
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?
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?
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?
Why would anyone care how the MAGs are related to each other? Maybe if you had some greater story to tell, but as such, I just don't see the importance. In the context of phylogeny, I think the only interesting results would be if you had some MAGs which were truly unique, like if they were representatives of new genera or whatever. For such cases you could have phylogenetic trees with your new species reps and wisely chosen reference genomes..
That’s a good point. I do have a few novel species in my dataset.