I'm seeking assistance with aligning multiple sequences using MAFFT. I've encountered a challenge as some of the sequences are on the forward strand, while others are on the reverse strand. I understand that for a successful multiple sequence alignment, all sequences need to have the same orientation. My confusion lies in whether this requirement implies that all sequences should be in the 5'-3' direction or if they should all correspond to the same strand (e.g., all sequences from the forward strand).

Thank you for your kind assistance.