[maker-devel] does MAKER modify input FASTA

[Anurag Priyam]

Is it possible that the input FASTA file (containing the genome that
is being annotated) and the FASTA sequences in the output GFF file
(containing the resulting annotations + the genome) be different?

-> It's fine if the ordering of the scaffolds, or width (for pretty
formatting) are different.
-> But, will MAKER add 'NNN' or change the case to indicate masking?
It doesn't seem so to me, but I have only one test set, so can't be
sure.
-> Is it possible to get masked genome out from MAKER?

-- Priyam