Mesquite's menus differ from window to window and vary depending
on the calculations being performed. In operating systems such
as Windows and Linux, each window has its own set of menus embedded
at the top, thus making it easy for the user to understand the
context — a particular window — in which the menu
item exists. Users of the Macintosh OS will see the screen menu
bar change depending on what window is at the forefront. On the
other hand, there is considerable duplication of menu items from
window to window, which reflects the fact that windows share context
to varying degrees, but which may be confusing to users of operating
systems with window-specific menus. We will not here take sides
about which menu paradigm is better, but note that Mesquite's
menu are firmly organized so as to reflect the heirarchical structure
of the calculations performed.
- Learning about menus
- Standard menu items
- Where to find menu items
Learning about menus
Mesquite menus include a few constant ones (File, Edit, Window)
and various other menus that change as different modules are used.
This situation could be confusing to the user. For instance, menu
items for particular modules may appear in different places depending
on the context.
Below is a list of the standard menu items that should appear
in most configurations of Mesquite. There will likely be other
menus and menu items in addition to these.
Mesquite can automatically generate documentation for the current
menu configuration and present it to the user as a web page.
This can be done by selecting the Menu & Control Explanations
menu item from the Window menu of Mesquite. Also, if
you hold down the Shift key while selecting a menu item, an
explanation of the menu item will appear in the explanation
are of the foremost window.
Standard menu items
- New Make a new file (as a
- New Linked File
Make a new file (linked to the current project)
- Open File...
Open file as a separate project (not linked to current project)
- Open Other
Get file from web server
- Link File... Open
file and incorporate into the current file (or home file of
- Include File... Open
file as linked (and hence sharing information with) the indicated
- Close File Close the file
- Close All —
Close all projects
- Close Window
Close the foremost window
- Save File
Save the file to disk.
- Save File As...
Save the file to disk under another name.
- Get Info...
Shows what is the current file and its location.
Save the file to disk under another name and with a format other
- Save Window As Text...
Save the text version of the window (visible by touching on
the Text tab of the window).
- Print Window...
Print the foremost window.
- Print Window to Fit Page...
Print the foremost window so as to fit within a page.
- Save Window as PDF...
Save the foremost window as a PDF image.
- Activate/Deactivate Packages
Change the configuration of modules
loaded. These menu items affect what modules, among those installed
in your copy of Mesquite, are actually loaded at startup. Most
configurations load only a subset of menu items, for instance
to simplify the interface.
- Use All Installed modules
On next startup, load all installed modules
- Choose Configuration
Choose the configuration of module packages loaded at next
- Delete Configuration
Delete user-defined configurations
- Define Configuration
Define a new configuration of modules to be loaded at startup
- Show Macro List Show list
of Macros available, and where available explanations as
to what each does.
- Edit Macro Information
Change name and explanation for user-defined macros.
- Show Macro List
Show list of Macros available, and where available explanations
as to what each does.
- Rename Log file —
Renames the current log file.
- Reset Menus
Forces rebuild of all menus. Useful on Windows because of a
bug in the Java virtual machine that occasionally scrambles
- Force Quit
Forces Mesquite to quit without the usual clean-up and checking
whether the file has unsaved changes. Should be used only in
emergency situations (e.g. if some calculation appears to have
- Quit Mesquite
Minimally functional. Undos most recent change to tree in tree
window. Not available for Character Matrix Editor and other
- Cut, Copy, Paste
Have their standard uses, though currently only deal with text.
Change the default font for the foremost window.
- Font Size
Change the default font size for the foremost window.
- Add AUTHORS block to File
Adds an AUTHORS block to the file, important for collaborative projects.
- New Generic Nexus Block —
Make and edit a NEXUS block for the file.
- Edit Mesquite script
Edit a Mesquite script contained in the file
- Edit Comment
Edit the comment about the file.
- Character Matrix Editor
Show a data editor for a character
- List of Characters
Show the list of characters
for a particular character data matrix
- New empty matrix...
Make a new, blank character data matrix
- Make New Matrix from
Make a new character data matrix
by copying an existing matrix or filling the matrix from a special
source (e.g., simulated characters)
- sources of matrices listed here
- List of Character Matrices
Show the list of available character data matrices
- List of Character Models
Show the list of available models of character evolution
- New Character Model...
Make a new model of character
- types of character models listed here
- Edit Character Model...
Edit an existing model of character
- Parsimony model sets
Show a list of the sets
of assignments of parsimony models for a particular character
- Probability model sets
Show a list of the sets
of assignments of probability models for a particular character
- Character sets
Show the character sets
for a particular character data matrix
- Inclusion sets
Show the character inclusions
sets for a particular character data matrix
- Character Partitions
Show the character partitions
for a particular character data matrix
- New Tree Window
Show a new tree window for a
particular set of taxa (multiple tree windows can be shown)
- Current Tree Window
— Bring an existing tree window to the
- List of Taxa
Show a list of taxa for a particular
set of taxa
- New Block of Taxa...
Make a new set of taxa
- List of Taxa Blocks
Show a list of the different sets of taxa
- List of Trees
Show a list of trees in a tree
block in the file
- New Empty Block of Trees...
Make a new empty block in which to store trees
- Make New Trees Block from
Make a new block of trees by copying an existing block or filling
the block from a special source (e.g., simulated trees)
- available sources of trees listed here
- List of Tree Blocks
Show a list of tree blocks in the project
- Multi Tree Window
— View several trees at once in window.
- List of Taxa Partitions
Show a list of taxa partitions that exist
- List of Taxon Sets
Show a list of the Taxon sets that exist
- Menu items to make new charts and other analyses are listed
- Menu & Control Explanations
Causes Mesquite to compose a
web page listing the menu items currently in the menu bar for
this window, and where available gives explanations for what
they do. Also lists the buttons currently in the window, and
where available gives explanations for what they do.
- Clone Window
Clones the foremost window. Useful to reproduce an existing
analysis then change it slightly. Cloned window will appear
exactly above original window; thus the clone should be moved
to view the original.
- Save Window As Macro
Save foremost window as a macro. This macro can later be used
to reproduce the window's appearance and analyses.
Execute the selected macro.
The "Show Snapshot" item displays the script that would be required
to return the foremost window to its current states; "Send Script"
sends a script to the foremost window.
- Bring All Windows To Front —
Brings all Mesquite Windows to the front.
- Current Windows —
Allows you to select current Mesquite windows to bring them
to the front.
- Mesquite Startup Window —
Makes the Mesquite startup window visible.
- Mesquite log — Makes
the Mesquite log window visible.
- Mesquite Projects and Files —
Makes the Mesquite projects and files window visible.
- Display License Shows the
license under which Mesquite is distributed.
- Mesquite Manual
Show home page of Mesquite manual
- Modules Loaded
Show web page of modules that are installed and loaded
- Keyword Search
Search for exact keyword among the names and explanations of
- Web Search
Search for exact keyword using the Google search engine.
- Scripting Commands
Show web page of available commands for scripting
- Active Module Tree
Show the entire employee tree of modules
- List Active Modules —
Write to the log a list of the entire employee tree of modules
- List Prerelease Modules —
Write to the log a list of any modules loaded that are labelled
as prerelease and substantive
- Show Developer Statistics
Write to the log some information useful for debugging.
Where to find menu items
Other menus come and go depending on which window is in front
and what calculations are in use. Thus, the standard Tree Window
has a Tree menu.
As the user requests calculations and output of results, the
menus change. The reason for this is that different menus are
appropriate in different circumstances. Thus, if the user requests
the Balls and Sticks method to draw trees, a menu item "Spot
size" appears in the Tree menu. Spot size controls the size
of the balls drawn at the nodes of the tree.
Exactly where a menu item appears may at first be confusing to
the user, but there is a certain logic to it that hopefully won't
be too obscure (technical details are available in the developer's
documentation). The "Spot size" menu item belongs
to the module that draws trees in the Balls and Sticks fashion,
since that module wants the user to be able to control the size
of the balls. That menu item appears within the menu of the modules
that employ it to draw trees. Since the Drawing menu belongs to
the module that coordinates tree drawing, and it is this module
that (indirectly) is employing Balls and Sticks to draw the tree,
the menu items belonging to Balls and Sticks appear in the Drawing
A module can also have its own menu, as does the tree drawing
coordinator. Thus, the menu items of a module (usually) appear
in the menu belonging to its closest employer module that has
its own menu. We say "closest" because sometimes a module
will have a menu item, but its immediate employer won't have a
menu to put it in. The menu item drifts upward in the employment
hierarchy until it finds an employer that has a menu that can
This system means that menu items appear in an appropriate context,
but that that context is not fixed because it depends on what
employer has a menu in which the item can be housed.