The basic logic of phylogenetic reconstruction is quite straightforward. Nature provides species. These species have a phylogenic history, but that history cannot be observed directly. There is only one true phylogeny. Inheritance from common ancestry produces similarity.
Evolutionary divergence produces differences.
We arrange the species according to similarities and differences. Unfortunately, Nature does not cooperate. Nature provides misleading and contradictory clues. Cladistic analysis using parsimony and numerous similarities and differences. The difficult job for phylogenetic reconstruction, like that for classification, is deciding which way of choosing characters is most reliable in any particular case.