This week’s tip of the week highlights the MEGA tools–MEGA is a collection of tools that perform Molecular Evolutionary Genetics Analysis. MEGA tools are not new–they’ve been developed and supported over many years. In fact, on their landing page you can see the first reference to MEGA was in 1994. How much computing were you doing in 1994, and what kind of computer was that on?
As they describe their tools on their homepage–here’s a summary:
MEGA is an integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence times, mining online databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.
But you can see they’ve progressed regularly and deeply since 1994, continuing to add new features and tools, and the current version is MEGA6. Although we usually focus on web-based interfaces, there are some tools that run on a desktop installation instead. So you will have to download and install MEGA to try it out, but the number of things you can do with it make it worth your time.
I decided to take a fresh look at MEGA because it was referenced in the gibbon genome paper that I’ve been perusing to find software tools in use by the genomics community. And I happened to find some training videos developed by the NIAID Bioinformatics team about using MEGA. Their focus in these videos is MEGA5, but much of the foundational information will be the same.
The first video illustrates a file conversion and preparation–getting your data into the right format for MEGA. I won’t embed that here, but when you are ready to kick the tires yourself you should have a look. I’ll jump right to the second video, that includes a bit more action about the things you can do with MEGA. This covers generating a neighbor-joining tree, and several subsequent options for modifying and saving it.
But this is just one aspect of what you can do with the MEGA tools. Be sure to explore the range of things you can do. Their documentation contains a section aimed at the “first time user” that can help you to understand various options you have. They also have sample data for you to try out the tools.
Tamura K., N. Peterson, G. Stecher, M. Nei & S. Kumar (2011). MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, 28 (10) 2731-2739. DOI: http://dx.doi.org/10.1093/molbev/msr121
Tamura K., G.Stecher, D. Peterson, A. Filipski & S. Kumar (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, 30 (12) 2725-2729. DOI: http://dx.doi.org/10.1093/molbev/mst197