One thing to keep in mind as you answer this question is that phylogenetics, like so many other subjects in science, is simply the study of a theory, and in this case, it is a theory that is very difficult to prove concretely.
Phylogenetics is the study of organisms which may have evolutionary relationships. When two organism are said to be phylogenetically related, in short, it is suggested that they stem from a common ancestor but have "branched" into two separate organisms through many years of evolution. One of the difficulties in proving organisms are phylogenetically related is the fact that the process by which organisms are determined to be such requires genetic data. Genetic data is only available for living organisms. Therefore, to link two (or more) organisms onto the same "phylogenetic tree" is merely a hypothesis based on events which are only assumed to have happened.
Under such restrictions and given that these are hypotheses only, organisms which are currently accepted as having a phylogenetic relationship are birds and reptiles. Is is believed by many scientists that birds and reptiles (though clearly very different organisms today), descend from one common ancestor.