How to customise colour codes for Multiple sequence alignment (MSA)?

I need to customise the colour code for protein multiple sequence alignment (MSA), However the existing R packages only supports the predefined colour codes, which are single letter based. But, I have to assign my own colour scheme for a pair of letters (amino acid). I have gone through the packages like ggmsa and ggplot2 etc., but failed to find the solution. I need to generate a figure as shown below,

I have followed the below script but could not serve my purpose,

tree = read.tree("tree.newick") 
msaplot(p=ggtree(tree), fasta = "msa.fasta")
msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "msa.fasta")

My fasta file is shown below,


My test tree file are shown below,


Kindly help me to do the same.

Thanks in advance.

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