Project background: I am trying to look at chemosensory evolution (GRs and ORs) across insect orders. I am specifically planning to look at GR and OR diversity between herbivore vs non-herbivore insect orders, look at selection and diversification rates along the branches between herbivore vs non-herbivore insect orders.
I have about 180 genomes that I have selected and downloaded from NCBI assembly (Genbank), most of which do not have annotation and I wanted to know the best way to bulk annotate these reference genomes so that I can get the list of proteins and genes in each of the reference genome so that I can then extract GRs and ORs from all the genomes.
I have been looking at Braker and EggNog but it looks like it is made for annotating novel genomes and might be slow to bulk annotate.
Thank you in advance!