Mesquite Help: Learning how to use Mesquite
Table of contents
Mesquite's documentation and other
learning aids
Because of Mesquite's complexity we have provided various aids
to help you discover and learn features:
Manual: This manual provides an introduction
to Mesquite, including instructions for accomplishing some analyses.
It resides in the docs subdirectory of the Mesquite_Folder
directory, and is also available from the Help menu while Mesquite
is running.
Search Features: Most windows have a small text
box (usually near the top of the window) beside the words "Search
Features" or "Search Data". When set to Search
Features mode (which you can request by clicking on the
little symbol until it shows "&" or "/"),
you can use this to find features and how to use them. Enter text
there and hit Return, and the text will be sought. There are several
modes, marked by different symbols:
-
— Search Features, AND: searches through information about
Mesquite's features and returns a description of those features
matching ALL of the search terms
— Search Features, OR: searches through information about
Mesquite's features and returns a description of those features
matching ANY of the search terms
(The Search Data feature
searches the current data file or project and returns objects (e.g.
taxa, characters, sequences) that match the search string.)
The results of the search are shown in the main Mesquite window
(shared by the Log window). The results may list modules, tools
or manual pages that match the search terms. If you touch on the
name of a manual, you may get a list of the contexts in which
this module can be used. (Please: we realize
that the search results can sometimes be long and difficult to
follow. Please give us your feedback as to what you would most
want to know in response to a search, so that we can improve this
feature.)
Example files: One of the best ways to learn
about analyses is via the example files, which are distributed
with the main Mesquite package and with various of the add-on
packages. The example files are present in the "examples" folder
of Mesquite_Folder. Some additional examples are outlined on the
Studies page.
Explanation areas: Explanation
areas at the bottom of each window may describe the window,
its contents, or the function of a selected button or other object.
If you hold down the Shift key as you select a menu item, an explanation
for it will (usually) appear in the explanation area of the frontmost
window. Explanations areas are also present in some dialog boxes.
Web Search: This menu item uses a web browser and the
Google Search engine to search for terms entered by the user.
Users may restrict their search to the Mesquite Manual if desired.
Mesquite FAQ: There is a preliminary Frequently
Asked Questions page.
Window information bar: The small
tabs near the top of each window allow you to select a view:
Graphics, Text, Parameters, Modules and Citations. The Modules
view in particular can help you learn about Mesquite calculations.
It shows the set of modules currently active in the analysis and
or graphics shown in the window. This is shown as a tree of modules
employing other modules (a bureaucratic hierarchy!). If you pass
the cursor over a module name, an explanation for it appears in
the explanation area at the bottom of the window. If you touch
on the name of a module, a menu will appear with choices to show
more information (if available). If there is a special manual
for the module, an extra label will appear that will link you
to the manual.
Additional web pages: Mesquite surveys modules
for information and composes a set of web pages. These web pages
list all the modules loaded, brief explanations as to what these
modules do, and the scripting commands these modules respond to.
These Mesquite-composed HTML pages are in a directory called "Mesquite_Prefs"
within a directory Mesquite_Support_Files, which
may reside in different places depending on your operating system.
If you can find these pages, you might want to store a bookmark,
or alias, or shortcut to one of them so that you can find them
again without going through Mesquite.
Menu & Control Explanations: The menu item Window>Menu
& Control Explanations causes Mesquite to compose
a HTML page summarizing the menu items or buttons for the current
window, and to show it to you.
Keyword Search: This menu item in the Help menu of Mesquite
provides a currently-primitive facility to search among the names
and explanations of all of the installed and loaded modules to
find a keyword. You could, for instance, search for "simulat"
to find all of the modules that might have to do with simulations.
Thus, if you want to learn about:
- Modules:
- Use the menu items in the Help menu to go to the
appropriate HTML pages for modules or packages. You can
also get to the HTML pages of packages by touching the banners
in the Mesquite startup window (the window named "About
Mesquite").
- Use the Search Features facility in each window
- Open the Modules view of the window of concern
(using the tab in the information toolbar) and move the
cursor over the names of the modules to see explanations
in the explanation area, or touch on their names to go to
their information pages composed by Mesquite.
- Menu items
- Hold down Shift as you select a menu item to make an explanation
for it appear in the explanation area of the frontmost window.
- Use the Menu & Control Explanations menu item
of the Window menu to make a web page summaring the
functioning of the menus and buttons for the foremost window.
- Buttons and tools:
- Touch on a tool in the tool palette to make an explanation
for it appear in the explanation area of the frontmost window.
- Use the Menu & Control Explanations menu item
of the Window menu to make a web page summaring the
functioning of the menus and buttons for the foremost window
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.
- Information bar of windows. The information
bar has various tabs 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.
Why Mesquite is complex
Mesquite has many options depending on what modules are installed
and loaded. Its modularity and flexibility allow for many possible
analyses, but also create challenges for the user (and the manual
writer). There are too many possible analyses for us to have yet
written instructions specifically for each. If the user wants
to perform some particular analysis, he or she may have to use
his or her puzzle-solving ability to figure out how to achieve
the analysis by combining Mesquite's various functions.
Why are so many choices? Why do some analyses assault you with
a guantlet of many dialogs? These are consequences of Mesquite's
flexibility. We have tried to protect you from complexity as much
as possible.
You may find a slightly different rhythm of thinking will be
needed when confronting Mesquite. For instance, suppose you wanted
to see how much the likelihood for a character varies if random
noise is added to the branch lengths of the phylogeny. If you
were lucky, there would be a macro or some menu item that would
build your desired analysis directly, but for this question there
isn't currently such a shortcut. What you'd like to see is a frequency
distribution of likelihoods calculated for the character over
a series of trees, each tree derived from some given tree by adding
random noise to the branch lengths. This sounds like a bar chart
(histogram), but which bar chart? It seems to concern characters,
so perhaps it is a Characters bar chart? No, each sample point
is a tree, and thus you should ask for a Trees bar chart. When
a dialog box asks you what value to calculate for the trees, what
do you say? The likelihood concerns a character, and thus you
respond "Tree value using character". In the next dialog,
you can choose character likelihood. You will also be asked what
source of trees. The trees are randomly modified by adding noise
to the branch lengths; therefore, choose "Randomly Modify
Tree" and for the particular modification, "Add noise
to branch lengths". Although this may seem complex, it does
allow you to design the analysis exactly as you wish. You may
use the example files, instructions in this and other manuals,
and the Mesquite discussion list
in order to learn how to do the analyses you need.
Features that help reduce Mesquite's complexity to the user are:
- Primary Choices: Submenus and dialogs boxes
with lists of alternative choices may have a small number of
choices listed then an item "Other Choices..." (if
a submenu) or a check box "Show Secondary Choices"
(if a dialog box). If these are selected, a larger number of
choices is offered, including the "secondary" choices.
This division of choices into the primary choices (the ones
we expect will be most frequently selected) versus the secondary
choices helps keep the commonly seen array of choices small.
(This division can be turned off in the Defaults submenu of the
File menu.)
- Macros: Mesquite can be instructed by a scripting
language. Macros can therefore be written or automatically
generated to script complex calculations. Macros appear in submenus
in the appropriate menu.
- Configurations: Even if many packages of
Mesquite modules are installed, you can ask Mesquite to load
only a subset of them. This allows Mesquite to startup more
quickly and to present a simpler interface (i.e., with fewer
options). You can control configurations using the submenu File>Activate/Deactivate
Packages>.