Documenting Your Work

Publication quality trees

The following video shows how you might generate graphics files of your trees for publication.

How to remember or document what you have already done?

With an interactive program having as many options as Mesquite, it can be difficult to remember what options are currently in effect. Three facilities help you keep track of what you've done.
  • The view modes of windows. The Window>View Mode submenu has various options that control alternative views of a window's contents. Some of these give information about the current calculations, the parameters in use, and details about the modules in use by the window.
  • The Log Window, available by selecting Mesquite Log in the Window menu, records commands given and messages relayed to the user. This text is also saved automatically to a file called "Mesquite Log" within the directory Mesquite_Support_Files.
  • Auto-scripting for file saving. When Mesquite saves NEXUS files, it automatically constructs a script that attempts to return an analysis to its current state. This not only allows a user to save a snapshot of an analysis, but the script itself can also be inspected to determine current parameters (in case that's not evident otherwise). Snapshot scripts can also be seen for individual windows, by selecting the appropriate item in the Scripting submenu of the Window menu.