Cladistic methods rely on assumptions about ancestral relationships as well as on current data.
Within the field of taxonomy there are two different methods and philosophies of building phylogenetic trees: cladistic and phenetic.
Cladistic vs. Phenetic
Phenetic methods construct trees (phenograms) by considering the current states of characters without regard to the evolutionary history that brought the species to their current phenotypes.
•For character data about the physical traits of organisms (such as morphology of  organs etc.) and for deeper levels of taxonomy, the cladistic approach is almost certainly superior.
•Cladistic methods are often difficult to implement with molecular data  because all of the assumptions are generally not satisfied.
•Computer algorithms based on the phenetic model rely on Distance Methods to build of trees from sequence data.
•Phenetic methods count each base of sequence difference equally, so a single event that creates a large change in sequence (insertion/deletion or recombination) will move two sequences far apart on the final tree.
•Phenetic approaches generally lead to faster algorithms and they often have nicer statistical properties for molecular data.
•The phenetic approach is popular with molecular evolutionists because it relies heavily on objective character data (such as sequences) and it requires relatively few assumptions.