MEGA

MEGA is a phylogenetic analysis package for use with protein and DNA sequences.

Currently, the software package is part of the bioinformatics Singularity container.

UFS HPC Usage Example

Follow these steps to start working with MEGA:

Before creating a qwiz or qvnc session, make sure that you have the bioinformatics container loaded as module:
```
$ module list
```
You should see the bioinformatics container listed as in the example below:
If the bioinformatics module is not loaded, load the current version of the container by issuing this command in the Terminal:
```
$ module load bioinformatics
```
Next, start a qwiz or qvnc session.
At this stage you may execute the GUI for MEGA by navigating to Activities > Show Applications > MEGA. See the below screen shots on how to navigate to and launch MEGA:
You should now be greeted with the MEGA GUI:

Please be aware that currently a bug in MEGA is causing the application to crash when doing an analysis run. This error is a bug in the GUI component (A GTK error). Note that this bug only affects the newest version of MEGA (Users using the old version through Wine doesn't need to worry about this error)

Thus, the current way to use MEGA is to setup the analysis in the GUI, save a .mao which can then be used to run the analysis using the command-line interface MEGA-CC. Note that you may do this setup process on your own computer and copy the saved .mao file over to the UFS HPC cluster (see this guide on how to copy files to the UFS HPC). The analysis can then be run with MEGA-CC. However, the following example shows how to do everything inside the VNC session:

In the MEGA main window, click on the Prototype button in the bottom right-hand corner:
Select the DataType of the sequences to be used in the analysis. In this example Nucleotide (non-coding) is selected. Click on the OK button to continue:
Next you can select the analysis you wish to perform. In this case select Phylogeny > Construct/Test Neighbor-Joining Tree:
Now edit the options for the analysis. In this case, the defaults are selected. Click on Save Settings:
The .mao file can now be saved:
You may now close the GUI window. Open a Terminal window and enter the following command, supplying the .mao file with the -a command-line option:
```
$ megacc  -a infer_NJ_nucleotide.mao -d Drosophila_Adh.meg -o demo
```
To learn more about the MEGA-CC command-line options, issue the following command:
```
$ megacc -h
```