Codon alignment with degenerate nucleotides?

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Is there a program that does codon alignments that works for degenerate nucleotides?

Also, how does PAML/codeml handle degenerate nucleotides?

The genome I am using to source some of the genes I want to use has degenerate nucleotides that represent differences between the two haplotypes.


paml


codeml


codon


alignment

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