MEGA provides options for performing various calculations relating to likelihood. In this tutorial, we will focus on the one you'll probably use most often, constructing Maximum Likelihood trees.
The “Drosophila_Adh.meg" data file, which is used in this tutorial, can be found in the MEGA/Examples folder (The default location for Windows users is C:\Users\UserName\Documents\MEGA7\Examples\. The default location for Mac users is $HOME/MEGA/Examples, where $HOME is the user’s home directory).
Constructing your Tree
Example 11.1:
Activate the "Drosophila_Adh.meg" file). If necessary, refer to Example 1.2 of the “MEGA Basics” tutorial.
Select Phylogeny | Construct/Test Maximum Likelihood Tree option from the main MEGA window launch bar.
The Analysis Preferences window will appear. For the Drosophila data file, you can choose between Nucleotide and Amino Acid substitution types. Select Amino Acid. Now, click on the drop-down for Models/Methods. Note the models available. Notice that the option to Select Codon Positions is disabled for Amino Acid sequences.
Change the Substitution Type to Nucleotide. The list of Models/Methods changes, showing only models which are applicable to nucleotide sequences. Select the Tamura-Nei model. Note that the option to Select Codon Positions is now available. Click on the button labeled Compute. A progress indicator will appear briefly.
The Tree Explorer will display the resulting Maximum Likelihood tree on the screen.
From the Tree Explorer toolbar, click on the i icon. The number of tabs shown here depends on the type of tree that was constructed. For a Maximum Likelihood tree, the tabs are General, Tree, Branch and Character States. Take a look at each to see the information they contain.
Saving your Tree
MEGA allows you to save trees in MEGA’s native format or in the Newick format.
Example 11.2:
From the Tree Explorer window, select File | Save Current Session from the main menu. In the Save As dialog, use the Save in drop-down to select the location then type in a name for the session in the File Name area. The tree will be saved with the MEGA ".mts" extension.
From the Tree Explorer window, select File | Export Current Tree from the main menu. In the Save As dialog, use the Save in drop-down to select the location then type in a name for the session in the File Name area. The tree will be saved in Newick “.nwk” format.
From the Tree Explorer window, select File | Exit Tree Explorer from the main menu. Click the Ok button without saving.