General Features

The following aspects of Zephyr should be considered when using it:

  • Characters that are set to excluded in your matrices will not be sent to the external program, or they will be sent but the external program will be told to exclude them.
  • The files to be analyzed by the external programs, and the resulting output files, are stored in a folder that will be created by Zephyr along side the original data file. These folders will have names such as "RAxML-2014.08.22-Run.1"
  • If you ask Zephyr to start an analysis on your local computer using script-based communication, and it successfully does so, and then you save your Mesquite file, Mesquite will save into the field enough details of the ongoing analysis such that if you close the file, and then later reopen it, Mesquite will reconnect to the external analysis and harvest the results.
  • If you need to stop an analysis, you can do so if you are doing either a CIPRes analysis, or a non-script-based analysis. However, if you have chosen script-based communication, there is currently no elegant way to stop the external program. Pressing the "Stop" link in the window on the right will stop Mesquite from monitoring the analysis, but not stop the analysis (again, this applies only to script-based communication). More details can be found on the Local Analysis page.