It’s a simple question but I would like to know if through PhyloPhlAn 3.0 can I construct a phylogenetic tree using only as input a collection of bacterial genomes deposited in public databases such as proGenomes, UHGG…?
My purpose is to construct a phylogenetic tree from de abovementioned databases and including it in a phyloseq object to perform beta-diversity metrics such as Unifrac distances.
Sure, you can! PhyloPhlAn won’t automatically download them for you though, the phylophlan_get_reference is just a convenient utility to download genomes from GenBank (for which we have a taxonomic label). But if you download the set of genomes from whichever public databases you’re interested in, then you can just provide those genomes to PhyloPhlAn for building your tree.