The primary source for variation between the species is the DNA code. In more dissimilar taxa more differences are expected in the DNA sequence and in the proteins for which it codes. Therefore both DNA sequences and protein structures have been used to determine the degree of similarity between species and thereby construct phylogeny trees.
With improvements in methods and reduced cost DNA sequencing is now nearly the only biochemical tool needed to construct animal phylogenies. Prior to the general availability of DNA sequencing several other methods came into prominence using different protein identification processes or DNA-DNA hybridization.