Downstream beta diversity analysis - tree generation for UniFrac metrics?

Hi,

We've been using Emu lately for our full-length 16S amplicon data generated on the Nanopore platform, and so far really are liking the results it's been giving us. Coming from the "short read world", one question I'm currently facing is how to go about doing phylogenetically-informed beta diversity analyses between samples. I thought I would post here to see if anyone had suggestions on how to go about generating a tree which I could then use (import into R via ape) for UniFrac analyses. I imagine I could just do multiple sequence alignment with the sequences I get in my samples, picking them out from the Emu database file I used (default DB), though this will be computationally expensive. Is there perhaps such an alignment that's already been done?

Happy to discuss further, but hoping the main aspect of my question is coming across well.

Thanks in advance,

Michael