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NERDS!!!
Nucleotides are the A, T, G and C bases that make up DNA.
Phylogeny is the study of evolutionary relationships between organisms.
Cladistics is about classifying organisms based on common ancestry.
Eukaryotes too: http://phenomena.nationalgeographic.com/2013/01/01/how-a-quarter-of-the-cow-genome-came-from-snakes/
If you use BovB genes for phylogeny, you’ll end up finding that cows are more related to snakes than other mammals.
I have no idea what you just said…
But I’m gonna assume it’s all science-y and stuff.
Use cladistics and go straight to phylogeny. Compare nucleotides at conserved parts of the genome to determine how distantly related two organism are.
Unless you are dealing with prokaryotes with horizontal gene transfer. In that case … good luck.