MSA with extended alphabet

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?

multiple sequence msa alignment

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updated 1.5 years ago by Mensur Dlakic

• written 1.5 years ago by retzl.bernhard •

1 answer

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

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written 1.5 years ago by Mensur Dlakic

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