Feature ids not present as tip names in phylogeny?

Hi @c.older,
No problem, you’ll get caught up in no time! To that end, check out this tutorial which might be of some help as it does a good job of explaining the whys and hows of various phylogeny analyses in qiime2. Eitherway you should make your own tree based on your rep-seqs. Which approach you choose is now the question, and your question above is basically asking to compare the reference-based approach vs. a de novo approach, the latter which is the focus of the link above. The usefulness of fragment-insertion is nicely demonstrated here and you can also read the paper cited there for more details too. Fragment-insertion does actually use a reference database (by default greengenes 13_8, but can be replaced with any other) and inserts de novo fragments for taxa not found there, though if a taxon is too far away from the nearest reference they may be dropped all together, therefore if you have a rare environment which may not be well represented in greengenes you should consider either using a different reference database or building a de novo tree.