Handling "?" and "N" in alignment

[elena-pt]

Good afternoon!

Could you please tell me if RAxML is adapted to correctly perceive "?" in alignment?
I built 2 trees: based on alignment with "N" and "?" and based on alignment with "N" (all "?" were replaced with "N"), and they are slightly different. I would like to use alignment with both types of characters, if possible.

Thank you in advance,
Elena