Pros and cons of amino acid structure vs DNA sequences for evolutionary comparison
Amino acid (protein) structure has its advantages over raw DNA.

Protein structure already has introns (noncoding regions) trimmed out which aren't obvious from a plain DNA string.

A protein can have different shapes (such as unbound/bound) or even folded/misfolded (as in the case of prions). DNA doesn't have a way of encoding these changes as they are dependent on substrates, environmental factors and available energy.

Visualizing the 3D structure of a protein can give insight into its functionality that you can't read off a DNA string.