Comparing groups of 16S rRNA sequences - how to?
If you want to make an all vs all with blast this can be helpful. You can create a blast database with your sequences and then search against itself.
makeblastdb -in 16S_sequences.fasta -dbtype nucl -out my_16S_sequences_db

blastn -db my_16S_sequences_db -query 16S_sequences.fasta -outfmt 6 \
       -out allvsall_16S.tsv -num_threads &quot;$(nproc)&quot;

If you want a percent identity matrix for a pairwise alignment you can try with this approach: https://www.biostars.org/p/220154/