Local Analyses
If you have asked Zephyr to conduct a local analyses (that is, the phylogenetic inference program resides on same computer as Mesquite), then Zephyr will create a folder on your hard disk (in the same directory as your data file), and store in there the files needed to conduct the analyses. This analysis directory will also serve as the repository for any files created by the analysis program.For local analyses you will need to specify how the external program is to be run, and what to do with the analysis directory. On the first Zephyr dialog box you will be presented with something like this (not all of these options are available for all external programs):
These options are discussed below.
Script-based versus direct communication
If "script-based analysis" is checked, then Zephyr will send a batch file containing a script of commands to the operating systems shell (e.g., cmd on Windows, the Terminal or bash shell on the MacOS, or the bash shell on Linux), and ask them to be executed. If it is not checked, then Mesquite will directly open the external program (RAxML, GARLI, PAUP, or TNT) and directly communicate with it without using a shell script.In general, direct communication (non-script-based) is better in that Mesquite has a more intimate connection with the external program. That allows Mesquite to be more directly aware of the other program's state (e.g., whether it is still running). It also gives Mesquite the ability to cause the other program to quit if the user decides to stop the analysis. The one advantage of using script-based analyses is that it allows Zephyr to reconnect with the running analysis is you have saved the Mesquite file while the analysis is going, closed the file, and then reopened it. This feature is not available with direct communication.
Terminal window visible
If you are using script-based communication on the MacOS, then you can ask to have the Terminal window visible so that you can observed the output from the analyses there. This also allows you to quit the external analysis as you then have control over it in the Terminal.Deleting the analysis directory
By default, the analysis directory is left in place after the analysis is done. This allows you to explore its contents in case you need to examine them. However, there are many circumstances in which you might prefer to have those directories deleted after each analysis is completed. The directory will be automatically deleted if you check "delete analysis directory after completion".Quitting the external program
You can stop Zephyr's monitoring of the external program by hitting the blue word "Stop" near the top of the Inferences in Progress section for that analysis:
This will stop Zephyr's monitoring, and will cause the external program to quit, unless you have chosen to do a script-based analysis. If you are using script-based communication, then you will not be able to stop the external program from within Mesquite. If you are using a Mac, and have chosen to have the Terminal window visible, then you can go to that Terminal window and either close it, or type Command-C into it. This should cause whatever program is running within it to quit. If you do not have the Terminal window visible, or are not using a Mac, then you will need to go into whatever application allows you to control processes on your computer (e.g., the Activity Monitor on the Mac or the Task Manager on Windows) and use that application to force the other program to quit.