Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution.
(to be submitted)
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
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Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
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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 data.

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.

Ex 9.1.2:   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 data file.

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.

Ex 9.2.2:   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.

Ex 9.2.3:   When the data file is active, the Input Distance Data Viewer is launched to display the contents of the data file.

We will now make a phylogenetic tree from the distance data.

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 command.

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 MEGA.

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 menu.