Is it possible to run panaroo_2_pagoo without removing "refound_"?

[emilywollmuth]

I am working with a divergent group of organisms, so I want to keep the genes refound by panaroo because I believe the core genome is being underestimated without them. My understanding is that the genes labeled "refound_" are not inherently a problem. Instead, it's the genes with the "stop" marker that are likely pseudogenes. Is there a way to run panaroo_2_pagoo and not remove all "refound" genes but to still remove "_stop" genes?

Alternatively, is it possible to use panaroo_2_pagoo and remove no genes or to make a pagoo matrix directly from a csv matrix instead of the long format data? If this isn't possible, I'll just need to convert the panaroo matrix to long format for pagoo to reformat it back into a matrix again.

Thanks for your work on this package. Pagoo is great and so easy to use!