The application is available as a GUI interface edition and a command line edition.The application can be used to build sequence alignments, estimate divergence times, infer phylogenetic histories, diagnose mutations, estimate rates of molecular evolution, and test evolutionary hypotheses.The application also comes with tutorials and example files to help first-time users get started.
It supports several popular DNA and protein sequence formats while giving you tools to examine the data and perform a variety of tests. MEGA is a necessary tool for those conducting research with DNA and protein sequences. Specifically, we have tested Mega X on Ubuntu 16.04.4 (with Unity desktop), Mint 18.1 (with Cinnamon desktop), and CentOS 7 (with GNOME desktop). Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. The numerous steps required to glean interpretable and actionable results from raw sequence data invariably require comparative analysis of molecular sequences to discover functional and adaptive genome differences. Molecular Evolutionary Genetics Analysis ( Mega ) software provides tools to conduct such analyses. Mega includes a large repertoire of programs for assembling sequence alignments, inferring evolutionary trees, estimating genetic distances and diversities, inferring ancestral sequences, computing timetrees, and testing selection ( Kumar et al. Over the last 25 years, Mega s use in evolutionary analysis has been cited in over one hundred thousand studies in diverse biological fields. But the ad hoc Windows-emulation solution is sluggish and relatively unstable when compared with the performance in MS Windows. Emulators cannot be used effectively for the latest 64-bit version of Mega that is built to handle memory-intensive analyses of large contemporary data sets ( Kumar et al. Therefore, Mega has been transformed into a cross-platform version that runs natively on Linux and Microsoft Windows. This advancement eliminates the Windows-only limitation of Mega, which has become particularly acute due to the increasing use of Linux in biological research. This transformation also paves the way for development of a MEGA X version for macOS in the near future. Extensive reprogramming of visual components was needed to compile cross-platform Mega, including the Alignment Explorer, Sequence Data Explorer, and Tree Explorer. ![]() The reprogramming was accompanied with visual modernization of many parts of the GUI ( fig. To provide a uniform user experience across computing platforms, many user interface elements have been implemented using the Chromium Embedded Framework (CEF), which is an open source framework based on the Google Chromium web browser core. With this framework, we have implemented GUI elements using HTML and JavaScript in Mega X desktop GUI ( fig. As a result, Mega X has the same look-and-feel in Windows and Linux. We are currently developing Mega X for macOS, which will share this user interface. Mega X can now be used in two modes: one for data analysis (ANALYZE mode) and another for prototyping (PROTOTYPE mode). Mega 6 Software Download Slide TheFig. 1. Open in new tab Download slide The Mega X main form has a modernized look-and-feel, but it maintains the familiar structure of the previous versions of Mega. A ) The top toolbar organizes the large number of analyses available in Mega X into logical groups accessed via drop down menus. B ) The bottom toolbar provides access to utility functions such as the help system, example input data files and application preferences. C ) Icons on the main form provide convenient access to input data and results explorer windows. These use the native widget set of the target operating system. ![]() F ) The redesigned Analysis Preferences dialog box for selecting options for data analysis, including ( G ) the number of threads to employ and ( H ) a Save Settings button for generating an.mao file for use with MEGA-CC for high throughput analysis. Fig. 2. Open in new tab Download slide The redesigned GUI elements in Mega X include explorer windows such as the ( A ) Sequence Data Explorer, ( B ) Timetree Wizard, and ( C ) Tree Explorer. This will greatly reduce the run time for computationally demanding inferences. Users can specify the maximum number of cores to deploy in the Analysis Preferences dialog box ( fig. G ). By default, Mega X uses all available cores, minus one, such that no 80 of RAM is consumed. Computational methods benefitting from calculation parallelization include those for selecting the best model for nucleotide or amino acid substitutions and bootstrap tests of molecular phylogenies employed with distance-based and parsimony-based methods. Users can already employ multiple cores during the heuristic search for the Maximum Likelihood (ML) tree in Mega. It will, however, work smoothly on previous versions of 64-bit Windows. We also provide a 32-bit version of Mega X for Windows for those with 32-bit computers. On Linux platforms, Mega X has been optimized and tested for use on DebianUbuntu and RedHatCentOS based distributions. Because users may customize their Linux environments easily, we recommend use of Mega X for Linux in tested desktop environments.
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