Build a pangenome from a multiple sequence alignment

[danimelsz]

Hello

I have a question. If I have 15 mitogenomes from different species aligned in .FASTA format generated in MAFFT, how can I build a pangenome from this alignment as it is (without re-aligning)? I guess we should use something like:

pggb -i test.fa --input-paf alignment.paf -o .

However, I do not know how can I generate this paf file. Is pggb able to build the pangenome based solely on a input FASTA alignment?

Thank you very much