MEGA, or Molecular Evolutionary Genetic Analysis, is a suite of tools that help explore and analyze DNA and protein sequences for evolutionary and population genetics. These include methods for multiple sequence alignment, tree inference, time trees, models of evolution, diversity metrics, selection metrics, ancestral state reconstruction, and evolutionary rates.

The application can be run both as a GUI (command mega) or a command line interface (command megacc). To run the GUI, we recommend connecting to Biowulf using NoMachine. The GUI can be used to run analyses and additionally create analysis options files (.mao files) that can be passed to the command-line application. This can be helpful for running large analyses with sbatch or swarm.

Reference:

• Koichiro Tamura, Glen Stecher, and Sudhir Kumar MEGA11: Molecular Evolutionary Genetics Analysis version 11 Molecular Biology and Evolution 38:3022-3027 (2021)

• MEGA Main Site
• MEGA Online Manual

This application requires a graphical connection using NX to run the GUI version

• Module Name: MEGA (see the modules page for more information)
• Singlthreaded. Multithreaded for ML phylogeny method.
• Run mega command to start the graphical user interface; megacc for the CLI
• Example files in $MEGA_EXAMPLES. When you start the GUI, example files will automatically copied to "/home/$USER/MEGA X"
• When running the GUI, you can safely ignore the following message:
  libGL error: MESA-LOADER: failed to open swrast: /usr/lib64/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib64/dri) libGL error: failed to load driver: swrast

The Blast and Genbank features in MEGA GUI will not work on Biowulf since compute nodes are behind a firewall and MEGA is not able to use proxies. We recommend installing the GUI on your desktop to access these features. You can save a MEGA data session file and transfer it Biowulf to reopen in MEGA in an sinteractive session

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load MEGA

[user@cn3144 ~]$ mega

Create a batch input file (e.g. MEGA.sh). For example:

#!/bin/bash
set -e
module load MEGA
megacc -a analysis.mao -d data.meg

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] MEGA.sh

Create a swarmfile (e.g. MEGA.swarm). For example:

megacc -a analysis1.mao -d data1.meg
megacc -a analysis2.mao -d data1.meg
megacc -a analysis1.mao -d data2.meg
megacc -a analysis2.mao -d data2.meg

Submit this job using the swarm command.

swarm -f MEGA.swarm [-g #] [-t #] --module MEGA