@microbesatsea @jongsanders @bactereedia @jmblanton If you have a set of genomes, the most highly-resolved way to do it is through pangenomics, in my opinion. Here is an example:
https://t.co/98H2X6q9HA (a reproducible workflow also exists).
See the phylogenomic and pangenomic workflows in anvi'o:
https://t.co/yZq1xKloEi
New paper from Yeoman used PATRIC's annotation service. Their genome is now available in PATRIC (https://t.co/16AOskiI1k).
https://t.co/qfhtKTza0L via @thePeerJ