I'm doing a metabarcoding analysis of both ITS and 16S targets.
I filtered the feature table to have only the most 50 representative Genera in a not quick way, since I could not extract the rep-sequences from a collapsed table.
Basically, I collapsed the table at the level 6, then looked for the frequencies of the first 50, went back to the original feature table and chose a much lower frequency (because the species when collapsed are less than the expected) to finally have a filtered table with the first 50 taxa. Using this feature table I then extracted the related sequences from the rep-seqs, aligned and created the tree.
I now would like to create a phylo tree with relative abundance among the sample, like the following one, but I have no idea how to do it.
Any help please?