Phylogenomic tree branch lengths are expressed in units of 'average substitution rate' (number of substitutions per site). Now, we can have substitution of amino-acids or nucleotides. Protein sequences are said to be more conserved.

I'm looking for a universal phylogenetic tree branch length unit, from which I could estimate average nucleotide substitution rate within the whole genome, and average substitution rate in the exome along the same lineage of taxa. This is equivalent to finding a scaling factor between average amino-acid substitution rate in the exome and average nucleotide substitution rate in the genome.