Comparative analyses of DNA and amino acid sequences is a powerful paradigm in biology, including evolution, ecology, development, and medicine. The Molecular Evolutionary Genetics Analysis (MEGA) software is a widely used tool to apply state-of-the-art methods for sequence analysis in these biological disciplines. MEGA provides an intuitive graphical user interface (GUI) to enable researchers to explore their primary data and results interactively, along with an integrated analytical engine that makes a large repertoire of evolutionary analysis methods easily accessible. MEGA is used by thousands of researchers in biology and has become a major teaching tool in universities worldwide. However, MEGA is primarily for use on Windows operating systems, which limits its utility and impact. The goal of this project is to (a) make MEGA cross-platform; (b) ready MEGA for community contributions and third-party expansion of functionalities; and (c) add a workflow GUI in MEGA to enable researchers to assemble pipelines and workflows that are becoming essential for rigorous, reproducible, and automated analytics in this era of big data. These developments will lead to a major enhancement of software infrastructure in biology and related interdisciplinary areas, all of which are critical in modern biological research. They will advance education through the development of tutorials, and benefit underserved populations through workshops and teaching.
Comparative analyses of DNA and amino acid sequences, a powerful paradigm in computational biology, have grown and adapted to the changing needs of biological sciences. Due to its increasing analytical complexity, successful application of the comparative paradigm requires efficient, sophisticated, and intuitive software. The Molecular Evolutionary Genetics Analysis (MEGA, now in version 7) software is among the most widely used tools for sequence analysis, as it provides a powerful and intuitive graphical user interface (GUI), giving researchers tools for exploring their data and visualizing results interactively, and placing a large repertoire of state-of-the-art evolutionary analysis methods at their fingertips. This "Development" proposal is to modernize and re-engineer MEGA using cutting edge software libraries and development philosophies. It will ensure that this vital community resource not only remains useful for the next decade, but also becomes cross-platform and extensible for community integration of new methods and tools. The project will leverage modern open source application development stacks and libraries, drawing upon web technologies (JavaScript, HTML5, and CSS) for a platform agnostic application, which will lead to an open source, cross-platform MEGA GUI that is ready for community contributions and third-party expansion of functionalities. It will also add a new workflow system (AppFlows) to enable researchers to assemble pipelines and workflows that are becoming essential for rigorous, reproducible, and automated analytics in this era of big data. The new AppDepot in MEGA will host add-ins and extensions (small and large) developed by community programmers by reusing MEGA-X components and core libraries. AppDepot will bridge the gap between computational/statistical method developers and biological users, as the large installed base of MEGA will immediately make new methods available to many to test and use. All of these results will be available from www.megasoftware.net .
