[suchire]

Except phylogeny generally was used to categorize how hereditarily related things were. Whether sequence alignment or physical taxonomy are better determinants is perhaps an open question in some cases, although I’m firmly on the side of sequence alignment, since DNA is an important component of inheritance

[Kaijo]

The side you are on has already won. Sequence data are universally accepted in systematics as the ultimate arbiters of evolutionary relationships, just delve into the modern classification of any extant group. One example of where molecular evidence overturned physical evidence long thought to be unambiguous, leading to a complete and essentially uncontested taxonomic overhaul: coprinoid mushrooms. Morphological characters are still used in paleontology for obvious reasons, but again within a higher-level framework provided by molecular phylogenetics.

[dekhn]

Really? Cool! This was still pretty much unresolved in 2003 when I worked in the area and I had been told people were still arguing about this recently.