How to handle gene duplication and loss properly #35

Hi,

CAGEE seems an incredibly interesting tool and the related published work is very interesting, congratulations to all the authors.
I was just wondering what is the best way to handle gene duplication and loss in the input data. is it suggested to identify the 'ancestral' copy that will have data for all the species, while the duplicated one will have lineage-specific data, and empty values for those species where the speciation event happened before the duplication event?
Best,
IG