ok. maybe that image will help us to communicate better because a language barrier. here is the phylogeny of the cytochrome c protein:
(image from britannica site)
you can see that the cytochrome c tree also fit with the creatures similarity in general. so for instance human and a monkey share more similarity on that protein than say human and a tuna. now, this similarity/difference (even the headline called “Phylogeny base on nucleotide difference”) comparison indeed give us a tree. and this tree indeed base on level of similarity\disimilarity. now, if i got it wrong again please tell me where im wrong and we will continue from there. i can also discuss about the non-functional sequence argument but lets focus each point at time.