How to run MetaPGN with MAGs

[Xiaolan89]

Hi,

I think this work is interesting and I got some bins affiliated with same genus from metagenomes recently. So I am trying to constructed pangenome network based on them. Should I treat them as isolated genomes or just assemblies from metagenome? And could I just use their nt sequences as input or I have to predict and annotate the genes then combine them into a single file?

Thanks in advance!