In the documentation, specification on clades is done with AA-changes - is this also possible with nucleotides?
Yes this can be done in augur clades - there’s some docs here and we use nuc mutations to define our SARS-CoV-2 clades.
There are also SNP typing PCRs for these SNPs - is it possible to automatically link this PCR-primers?
Augur doesn’t consider these, but Nextclade has the ability to identifying mutations in (specified) primer sites. There may be better tools to answer your exact question however.
Best,
james