I have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I already know to be reliable phylogenetic marker, where present, but the scale of my current dataset makes it a bit daunting.
Is there any software for taxonomic assignment that you could recommend? It's fine if it requires command line use. There are so many options listed online that I didn't even know where to start... Please and thank you.