Hi All

Could anyone guide me on how to generate a rooted a nexus file for protein Sequences and a rooted tree? I have both the alignment and the tree. My problem is how to root the tree in the nexus file to be able to use for FADE analysis in Datamonkey.org or Standalone version of Hyphy. If someone has ever run the FADE analysis, could he get me their nexus data file so as I use it as a template to generate mine?

Thank you