I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately.
Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this a genus', 'is this a separate genus', 'is this sequence actually in the order of interest'. It feels like a lot of what I do is repetitive and could be automated more. In particular, it feels like there should be a simpler way for having an assemble view at sequence similarity rather that calculating a Percentage Identity Matrix and then putting it in Excel with conditional formatting. I'm imagining something like this clustering diagram for species (https://www.researchgate.net/publication/360738216/figure/fig4/AS:1182363421806594@1658908815491/The-t-SNE-clustering-of-bacterial-genomes-in-the-code-RA-space-at-different-taxonomic.png), but for sequences instead (using sequence similarity values, at least). Still, I can't seem to find something like that for 16S rRNA that's as visually compelling (or even as visually helpful as my Excel sheet). There are a number of programs for clustering OTUs, but the ones I've encountered don't seem to have a graphical / interactive interface.
Does something like this exist? Thank you for your time!