Shame on You
Nope. I think the argument about birds and dinosaurs has moved on to other aspects. Discovery of true dinosaurs with feathers has caused a shift. I doubt anyone is willing to go out on a limb and say feathers evolved independently twice.
There is a problem with cladistics and viruses: horizontal transfer of genetic information. You have no guarantee of getting a phylogenetic tree. (Technically, it becomes a directed acyclic graph, or dag. Viral heredity can present problems even Cleopatra VII lacked.) XMRV seems destined to break with human conventions in this area also.