prank transform codons to ambiguities

[chodon]

I am wondering if there is a switch (or if a switch might be generated) so that prank does not transform codons that have a single ambiguity into all Ns.
i.e. if a codon has AYC - after codon align, the codon will be NNN.

I tried to use the -keep switch but prank exited because 'Sequences don't seem to be aligned. Exiting.', so it seems that prank will not be able to align this file because -keep only works on previously aligned files? Hoping to keep as much data as possible. Thanks!!