GTDB Forum

Data for phylogenetic placement of 16S amplicons?


I had the idea of adding phylogenetic placement of 16S amplicon in our denoising pipeline using GTDB data, but I can’t find the SSU alignment and tree that I thought I had seen before. Have I overlooked the files? (Representative genomes would suffice.)

As an alternative, I thought of using GTDBtk, but that seems to be only protein sequences.

My last alternative is of course to download the representative genome SSU sequences, align and estimate a tree myself with fasttree. Would feel better with something official.


Sorry, we don’t provide a SSU alignment or tree. GTDB-Tk is specific to the concatenated protein sets used to infer the GTDB archaeal and bacterial reference trees.