Difference between revisions of "MEGA"

Latest revision as of 16:25, 8 January 2018

Description

From the MEGA web site: MEGA is sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations.

Version

7.0.26-1

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/7.0.26-1

See Modules for more information.

Running MEGA on CIRCE/SC

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.

Using MEGA on the command line

Once connected to CIRCE/SC, you can open MEGA (either megacc or megaproto) using the steps below:

[user@login0 ~]$ module add apps/mega/7.0.26-1
[user@login0 ~]$ megacc 
[user@login0 ~]$ megaproto

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

@@ Line 1: / Line 1: @@
 == 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.
+''From the MEGA web site'': MEGA is sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations.
-* [http://www.megasoftware.net/ MEGA Home Page]
+{{AppStandardHeader|7.0.26-1|mega}}
-== Version ==
+{{AppRunningOnAll}}
-*4.02
+=== Using MEGA on the command line ===
-== Authorized Users ==
+Once connected to CIRCE/SC, you can open MEGA (either megacc or megaproto) using the steps below:
-*<code>CIRCE</code> account holders
+<pre style="white-space:pre-wrap; width:40%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ module add apps/mega/7.0.26-1
+[user@login0 ~]$ megacc
-== Platforms ==
+[user@login0 ~]$ megaproto</pre>
-*<code>CIRCE</code> cluster
-== Running MEGA on CIRCE ==
-The following describes what is necessary to run MEGA on CIRCE.
-=== [[Modules]] ===
-MEGA requires the following module file and some prerequisites to run:
-*<code>apps/mega/4.02</code>
-=== 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.
-<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
-[johndoe@login1 ~]$ mkdir /work/j/johndoe/mega
-[johndoe@login1 ~]$ cd /work/j/johndoe/mega
-[johndoe@login1 mega]$ /opt/apps/mega/4.02/install-mega</pre>
-=== Starting MEGA ===
-Before you login to <code>CIRCE</code>, you need to make sure you have X11 Forwarding enabled. If you’re logging in from a UNIX/Linux system, you will need to do the following:
-<pre style="white-space:pre-wrap; width:25%; border:1px solid lightgrey; background:#000000; color:white;">
-ssh -Y user@circe.rc.usf.edu</pre>
-&nbsp;<br>
-Simply type <code> mega </code> at the command prompt AFTER loading the proper module (see above) in your terminal window. If you have properly configured an X11 session, you should see the full MEGA interface. If this is your first time using MEGA, you will need to follow the on screen instructions for the Mozilla ActiveX plugin and then MEGA should load normally.
-For Windows, Mac, and Linux users, MEGA can also be launched through the CIRCE Desktop Environment using a terminal. For more information about the CIRCE Desktop Environment, please see our [[CIRCE Desktop|CIRCE Desktop Environment]] documentation.
-=== Additional Documentation ===
+{{Documentation}}
 * MEGA Home Page
 ** http://www.megasoftware.net/
 {{ReportingBugs}}