Limitations

=Limitations=

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*