There are many limitations in the current version of Zephyr. Among them are:
  • The external program must be running on the same computer as Mesquite
  • You can not elegantly stop the external program from within Mesquite
  • If the external program stops with an error, Zephyr usually does not recognize this
  • There are several options in RAxML that are not supported in Zephyr
  • Zephyr only supports a few options in PAUP*