Is the general time-reversible model bad for molecular phylogenetics?
  The general time reversible model (GTR) is presently the most popular model used in phylogentic studies. However, GTR has an undesirable mathematical property that is potentially of significant concern. It is the purpose of this article to give examples that demonstrate why this deficit may pose a problem for phylogenetic analysis and interpretation. 
Jeremy Sumner, Peter Jarvis, Jesus Fernandez-Sanchez, Bodie Kaine,   Michael Woodhams, and Barbara Holland
q-bio.PE math.ST q-bio.QM stat.TH