MEGA

Description

From the MEGA web site: MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

Version

• 4.02

Authorized Users

• CIRCE account holders
• RRA account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Modules

MEGA requires the following module file to run:

• apps/mega/4.02

• See Modules for more information.

Running MEGA on CIRCE

The MEGA user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

• Note on CIRCE: Make sure to run your jobs from your $WORK directory!
• Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Installing MEGA

Prior to the first time running MEGA, you will need to install the application to your work directory. This is necessary because the application attempts to writes configuration settings to the application directory. Because of this behavior the program works much better when it is copied to a users work directory.

[johndoe@login1 ~]$ mkdir /work/j/johndoe/mega
[johndoe@login1 ~]$ cd /work/j/johndoe/mega
[johndoe@login1 mega]$ /opt/apps/mega/4.02/install-mega

Starting MEGA

Establishing a GUI connection to CIRCE/SC

To use MEGA, you will need to connect to CIRCE/SC with GUI redirection, either using:

• CIRCE/SC Desktop Environment
• SSH with X11 redirection
  • If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:

    • [user@localhost ~]$ ssh -X circe.rc.usf.edu

      or

    • [user@localhost ~]$ ssh -X sc.rc.usf.edu

Once connected to CIRCE, you can open MEGA using the steps below:

[user@login0 ~]$ module add apps/mega/4.02
[user@login0 ~]$ mega

Documentation

Home Page, User Guides, and Manuals

• MEGA Home Page
  • http://www.megasoftware.net/

Reporting Bugs

Report bugs with MEGA to the IT Help Desk: rc-help@usf.edu