Trying to use a qiita study with multiple 16S prep templates, question about merging seqs.fna for building phylogenetic tree

Just to complement @tomasz's reply. Note that you can create a meta-analysis (combine all the bioms) and generate a single BIOM for all the studies, once you have that file, you can follow this example to get a phylogenetic tree: Importing deblur data from QIITA - #15.