Please use the main Datamonkey.org page to run GA-branch analyses.

You may also download two HyPhy batch files (updated on Nov 21st, 2006) to perform the analyses locally from [here]. Please note that an MPI cluster and and MPI build of HyPhy are required to run a GA branch analysis. The README.pdf file included with the distribution gives details on how to run the analyses and interpret the results thereof.