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Finding the differences in cytochrome c amino acid sequence?

I am needing to make a phylogenetic tree that reflects the evolutionary relationships of the organisms based on the differences in their cytochrome c amino acid sequences. I just cannot figure out what the differences do, or what the numbers change.

As in, a snake has the number 20 compared to a horse. Where 20 stands for # of amino acid differences in cytochrome. What does this number mean, and why?
Thank you!

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