text: user4401: 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!
  
  user3848: My recommendation is MegaX. It's the closest thing in phylogenetics to an all encompassing GUI.
  
  This has a nice visual alignment editor which highlights conserved, variable and parsimonious sites.
  It will produce distance matrices based on any number of criteria, e.g. % homology, Jukes-Cantor, Kimura-2 parameter etc ...
  Good for bootstrapping distance-calculations as well as can perform ML based tree building methods with full parameterisation.
  Nice tree visualisation, which can be edited, switched to viewing bootstrapping (if performed), or to branch genetic distances (again under any distance criteria, e.g. %age homology etc ..). It does loads of other stuff, which in this case are not needed.
  
  You can export the tree and import into FigTree to produce collapsed clades represented by coloured triangles. In summary for easy GUI stuff MegaX, then FigTree.
  There are no PCA/MDA based analysis for 16S sequence data because eiganvalue-based calculations would override lots of theory involved in point mutation modelling and the resulting trees. I could replicated the PCA output in the question with sequence data, its not hard to do - but it's not publishable.
  
original_text: 4401: <p>I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately.</p>
  <p>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 (<a href="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" rel="nofollow noreferrer">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</a>), 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.</p>
  <p>Does something like this exist? Thank you for your time!</p>
   3848: <p>My recommendation is <a href="https://www.megasoftware.net" rel="nofollow noreferrer">MegaX</a>. It's the closest thing in phylogenetics to an all encompassing GUI.</p>
  <ol>
  <li>This has a nice visual alignment editor which highlights conserved, variable and parsimonious sites.</li>
  <li>It will produce distance matrices based on any number of criteria, e.g. % homology, Jukes-Cantor, Kimura-2 parameter etc ...</li>
  <li>Good for bootstrapping distance-calculations as well as can perform ML based tree building methods with full parameterisation.</li>
  <li>Nice tree visualisation, which can be edited, switched to viewing bootstrapping (if performed), or to branch genetic distances (again under any distance criteria, e.g. %age homology etc ..). It does loads of other stuff, which in this case are not needed.</li>
  </ol>
  <p>You can export the tree and import into <a href="http://evomics.org/resources/software/molecular-evolution-software/figtree/" rel="nofollow noreferrer">FigTree</a> to produce <a href="https://www.researchgate.net/profile/Mariana-Louro/publication/350894395/figure/fig3/AS:1013091672281097@1618551285234/Maximum-likelihood-phylogenetic-condensed-tree-calculated-using-aligned-concatenated.png" rel="nofollow noreferrer">collapsed clades represented by coloured triangles</a>. In summary for easy GUI stuff MegaX, then FigTree.</p>
  <p>There are no PCA/MDA based analysis for 16S sequence data because eiganvalue-based calculations would override lots of theory involved in point mutation modelling and the resulting trees. I could replicated the <a href="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" rel="nofollow noreferrer">PCA output</a> in the question with sequence data, its not hard to do - but it's not publishable.</p>
  