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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.

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You could take a look at kraken2 It should fit your purpose.

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    $\begingroup$ yes, kraken2 performed well in an independant benchmark lemmi.ezlab.org $\endgroup$
    – Chris_Rands
    Commented Aug 12, 2020 at 21:04
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    $\begingroup$ It does work well, but it's less accurate at lower taxonomic ranks (as most tools are) $\endgroup$
    – aLbAc
    Commented Aug 14, 2020 at 9:52
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If you like blast, maybe you can try DIAMOND - the authors claim it's much faster than BLAST.

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