Build phylogenetic tree from a database


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.

Thank you,


Hello David,

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.

Many thanks,