Hello @Pmoa,
Welcome to the 
forum!
I am not sure how to build a SeppReferenceDatabase from FeatureData[Sequence], I have looked into it before and I think you can't. Here is another thread on the forum taking about this issue
But you can just build a phylogeny using you rep-seqs using align-to-tree-mafft-fastree. Here is an example from the “Moving Pictures” tutorial — QIIME 2 2022.2.0 documentation.
Hope this helps!
