Hello everyone! I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding genes, every fasta file includes genes from many species that are orthologs/paralogs. These genes even in the same species may use different genetic codes. My goal is to align the sequences, codon alignment, and afterwards to create N-J trees. For the whole process I work on MEGA11. I cannot organize the species-genes into groups with common genetic codes because I need all of them in the tree. One option, to my mind at least, would be the alignment not in codon but in DNA,or another option is to align their protein sequences or lastly a third option could be the change of the sequences in order to get rid of the stop codons and afterwards to use one common code for everything, by doing that I know that I will lose some info but at least I can work.Do you have any idea how to overcome this obstacle? Do you agree with any of this options? Thank you in advance!