In this example, we will conduct two different tests of reliability using protein-coding genes from the chloroplast genomes of nine different species.
The data file “Chloroplast_Martin.meg” 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).
Bootstrap Testing for a Neighbor-Joining Tree
Example 5.1:
Activate the "Chloroplast_Martin.meg" file. If necessary, refer to Example 1.2 of “MEGA Basics”.
On the main MEGA window task bar, select the Phylogeny | Construct/Test Neighbor-Joining Tree option.
The Analysis Preferences window appears on the screen. For the Model/Method, select p-distance. Select Bootstrap method for the Test of Phylogeny option.
Click Compute to accept the default values for the rest of the options. A progress indicator provides the progress of the test as well as the details of your analysis preferences.
Once the computation is complete, the Tree Explorer appears and displays two tree tabs. The first tab is the original tree and the second is the Bootstrap consensus tree.
To produce a condensed tree, use the Compute | Condensed Tree main menu command from the Tree Explorer window. You can further manipulate the appearance of the condensed tree here. To change the cutoff value, select the View | Options menu command and click the Cutoff tab. For now, keep the Cut-off value at 50% and click the OK button.
This tree shows all the branches that are supported at the default cutoff value of BCL ³ 50. Select the Compute | Condensed Tree main menu command and the original NJ tree will reappear.
From the Tree Explorer window, select the Image | Save as PDF File option and save a PDF image of the tree to a convenient location.
From the Tree Explorer window, select the File | Exit Tree Explorer command to exit the Tree Explorer. A warning box will inform you that your tree data has not been saved. Click Ok to close Tree Explorer without saving the tree.
Interior-branch testing for the Neighbor-Joining Tree
For neighbor-joining trees, you may conduct the standard error test for every interior branch by using the Interior branch test of phylogeny.
Example 5.2:
From the main MEGA window, select Phylogeny | Construct/Test Neighbor-Joining Tree from the launch bar.
In the Analysis Preferences dialog, make sure the Substitutions Type option is set to Amino Acid and the Model/Method is set to p-distance. Set the Test of Phylogeny option to Interior-branch test.
Click Compute to begin the computation. A progress indicator window will appear briefly. When the tree appears, confidence probabilities (CP) from the standard error test of branch lengths are displayed on the screen.
Compare the CP values on this tree with the BCL values of the tree that you saved as a PDF file in the previous exercise.
Now close the Tree Explorer by selecting File | Exit Tree Explorer from the main menu. Close the current data by clicking the Close Data icon on the main MEGA window.