Constructing Trees from Distance Data
This example introduces
procedures for selecting options from menus, opening files in the read-only
mode, activating a distance data file, and building trees from the distance
Ex 9.0.1: Start MEGA by double-clicking on the MEGA
desktop icon, or by using the Windows start-menu to click on the MEGA icon
located in the programs folder.
Ex 9.0.2: A Splash screen appears,
which displays the current version of MEGA.
Ex 9.0.3: The Splash screen automatically
disappears, and the MEGA application becomes available.
In this example, we use the data in the Hum_Dist.meg file. Although we will not edit the file, we
will use MEGA's built-in text editor to examine its
contents before we proceed further.
Ex 9.1.1: Click on File menu to expand the menu
options. Click on the menu item labeled Text Editor, or press the F3 key
to activate the built-in text editor.
Use the Text Editor to view the
contents of the Hum_Dist.meg file. To open a
file with the Text Editor, click on the folder icon below the main menu
or on the File menu item, then choose Open
from the expanded menu. You may also use the key combination
Ctrl+O to open a file. All of these options
will lead you to a standard Windows open file dialog box. Use this dialog box
to locate the Examples folder found in the MEGA installation directory,
and open the Hum_Dist.meg file. After
you open the file with the dialog box, you will see the file contents displayed
in the Text Editor window.
Ex 9.1.3: Examine the contents of the data file and
then exit the Text Editor before proceeding with data analysis. Select
the File menu item from the Text Editor ‘s menu,
and click Exit from the expanded menu. If the editor asks you if you
would like to save your changes, select No.
style='mso-bidi-font-weight:bold'>A data file must be activated before an
analysis can be performed. (Note that opening a file for browsing or editing is
different from activating it for analysis).
Now we will activate the Hum_Dist.meg
Ex 9.2.1: You can activate a data file by using the
link titled “Click me to activate a data file” in the main application window,
or by selecting the File menu item from the main menu and clicking the Open
Data option from the expanded menu. You can also press the F5 key.
All of these methods will display a standard Windows open file dialog box.
Use the open file dialog box to locate and
open the Hum_Dist.meg file located in
the Examples folder. After you have selected the file for opening, a
progress indicator will appear briefly.
When the data file is active, the Input Distance Data Viewer is launched
to display the contents of the data file.
will now make a phylogenetic tree from the distance
Ex 9.3.1: Switch back to main MEGA application window. From
the expanded menu in the Phylogeny menu, select the Construct Phylogeny|Neighbor-Joining
Ex 9.3.2: A confirmation Analysis Preferences window will appear, indicating that MEGA is
ready to conduct the requested analysis. Click on the button labeled “Compute.”
A progress meter will appear briefly.
Ex 9.3.3: The Tree Explorer will display a
neighbor-joining tree on the screen when the analysis completes.
To exit the Tree Explorer, select the File
menu item from the Tree Explorer menu and click the Exit Tree
Explorer option from the expanded menu. The Tree Explorer will ask
you if you would like to save the tree data. If you save the tree, you can use Tree
Explorer to view and manipulate it in the future.
With this, let us end this session of
Ex 9.4.1: Go to the File menu and click on the Close
Data command. The program will inquire if you would like the active data to
be closed. Select “Yes.”
Ex 9.4.2: To exit MEGA, press Alt
+ X, or select the Exit command from the expanded File