This tutorial illustrates procedures for building phylogenetic trees using distance data.
The Hum_Dist.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:\Program Files\MEGA\Examples. The default location for Mac users is $HOME/MEGA/Examples, where $HOME is the users home directory).
Making a Phylogenetic Tree from Distance Data
Example 10.1:
Activate the "Hum_Dist.meg" file. If necessary, refer to Example 1.2 in the MEGA Basics tutorial.
From the main MEGA window, select Phylogeny | Construct/Test Neighbor-Joining Tree from the launch bar.
The Analysis Preferences window will appear. For distance data files, all of the options shown here cannot be changed. Click on the button labeled Compute. A progress meter will appear briefly.
The Tree Explorer will display a neighbor-joining (NJ) tree on the screen when the analysis completes.
From the Tree Explorer launch bar, click on the i icon. The number of tabs shown here depends on the type of tree that was constructed. For a Neighbor-Joining tree, the tabs are General, Tree and Branch. Take a look at each to see the information they contain.
Saving your Results
MEGA allows you to save trees in MEGAs native format or in the Newick format.
Example 10.2:
From the Tree Explorer window, select File | Save Current Session. In the Save As dialog, use the Save in drop-down menu to select the location, and then type in a name for the session in the File Name area. The tree will be saved with the MEGA ".mts" extension.
Now, 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. In the File Name area, type a name for the session. The tree will be saved in Newick format with the ".nwk" extension.
Go to the File menu and click on the Exit Tree Explorer option.