Seed plant phylogeny: Demise of the anthophyte hypothesis?

@article{Donoghue2000SeedPP,
  title={Seed plant phylogeny: Demise of the anthophyte hypothesis?},
  author={M. Donoghue and J. Doyle},
  journal={Current Biology},
  year={2000},
  volume={10},
  pages={R106-R109}
}
Recent molecular phylogenetic studies indicate, surprisingly, that Gnetales are related to conifers, or even derived from them, and that no other extant seed plants are closely related to angiosperms. Are these results believable? Is this a clash between molecules and morphology? 
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