Changing distance matrix to scoring matrix to use in alignment software ? (attempt to aligning monomers)

Question

[Elephantdumbo]

Hey everyone, I would like to align monemers based on tajima-nei distance. I have already generated the distance matrix and the monemers have the same alphabet as amino acids

For example 2 sequences I have would be.

seq1 RAKGKGTGKGKGV

seq2 RKGAKGVNMKG

I am trying to use muscle and use a custom matrix, but I am having trouble converting distance matrix to scoring matrix

Do you guys have any suggestion how to do that ?

Thank you so much