I have some information for future applicants to the Joint Carnegie Mellon University - University of Pittsburgh Ph.D. Program in Computational Biology. I suspect this also applies to the Joint CMU-Pitt Molecular Biophysics and Structural Biology Graduate Program, but I don't know for sure. I should note that some of this may be in the CPCB handbook, but I know that some of it is not. I thought it would be best to list all the differences I heard about today for the benefit of future applicants who search for information in the forums on this program in future cycles.
I found out today that applicants are admitted to either CMU or Pitt based on their interests and the primary appointments of the PIs they are interested in working with / the PIs who are interested in working with them. It turns out this makes a difference for the application process. Pitt requires that all North American applicants interview at the institution before an offer can be extended, while CMU does not. Consequently, CMU admitted students receive offers earlier and without an interview, while Pitt admitted students must come to an interview before an offer can be extended. This is why 90-95% of Pitt admitted students receive an offer if they interview.
Where the student is admitted also affects the offer that is made. CMU does not provide health insurance, and it does not waive any fees. Pitt does both of these things. Consequently, the stipend for CMU admitted students is about $3000-$4000 higher than it is for Pitt admitted students. The coordinators of the program are responsible each year for going through all expenses and payments and making sure that the package offered to all students in the program is worth the exact same amount.
The thesis lab selection process is also different for CMU and Pitt students. Pitt students may either elect to start working in a lab right away if they know for sure who they want to work with, or they have the option of doing three four-week rotations in the first semester. Conversely, I believe CMU students are required to listen to talks given by each faculty member in the program who is taking students. After this is done, each student submits a summary of his or her research interests and PIs he or she is interested in working with, and the PIs submit lists of students that they are interested in working with. Students are matched with PIs based on this information.