There may be times when you want to make changes to a data file. With the MEGA Alignment Explorer, you can rearrange the taxa, delete blocks of taxa or delete blocks of sites. The altered data file can then be saved in either MEGA or FASTA format.
The “Chloroplast_Martin.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).
Using Alignment Explorer
Example 12.1:
From the main MEGA window, select Align | Edit/Build Alignment. Select Create new alignment | DNA. Then click Data | Retrieve sequences from a file and press the Ok button.
In the Open window, find and select the "Chloroplast_Martin.meg" file.
Rearranging Data
Example 12.2:
In the Alignment Explorer window, click the row header for the row named Pinus. Hold the left mouse button down and drag the row up, then release the mouse button when the position indicator is just below the Porphyra row.
Deleting rows
Example 12.3:
Now, click the mouse to highlight Porphyra. Select Edit | Delete on the main menu of the Alignment Explorer. Do the same for the row Pinus.
Deleting sites
Example 12.4:
Click on the horizontal scroll bar at the bottom of the Alignment Explorer window. Drag it all the way to the right. Now click on any cell in the last column. Notice that the Site # display changes to show the highest-numbered site, 11039.
You can delete blocks of sites in the same way that you can delete rows of data. Click on the gray header above any column of sites, hold down the left mouse button and drag across to any other column header to select multiple columns. On the toolbar, click the X icon to delete the selected sites.
Save the altered data file
Example 12.5:
On the Alignment Explorer menu, click on Data, and then select Export Alignment. Choose either MEGA format, FASTA format, or the PAUP format. In the Save As window, select the folder in which you want to save your data file and then type a name in the File Name area. Click the Save button.
Close the Alignment Explorer and click Ok without saving.