Codon alignment with degenerate nucleotides?
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16 months ago
DNAlias ▴ 40

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 • 426 views
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