Hey, I need a multiple sequence alignment with an alphabet containing 60 characters. But most tools only support standard amino acids. Has anyone a suggestion or a workaround?
I think it is unlikely you will find a pre-packaged solution to that problem. At the very least you will have to devise a scoring matrix (AKA substitution matrix).
Different programs will have their own requirements regarding the scoring matrix. For MAFFT they are listed at the following link:
https://mafft.cbrc.jp/alignment/software/textcomparison.html
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6