2/21/2024 0 Comments Gtr evolution download![]() Rapid relaxed-clock methods for estimating divergence times are becoming popular because they are feasible and efficient for large contemporary sequence alignments ( Tao, Tamura, Kumar, et al. ![]() Methodological Additions Expansion of Relaxed-Clock Dating Facilities Here, we present key methodological additions and technical improvements in MEGA that comprise version 11. With both 32- and 64-bit versions of MEGA currently available for use on the command-line and GUI, MEGA is now a suite of applications that responds to the variety of computing environments currently used by researchers in molecular evolution and phylogenetics. MEGA-CC was released for use as a command-line program to address the growing need for batch processing of many data sets and integration into analysis workflows ( Kumar et al. 2013), and stepped up to 64-bit architecture ( Kumar et al. 2001), became multithreaded and incorporated multicore parallelization for various calculations ( Tamura et al. It advanced from 16-bit to 32-bit ( Kumar et al. MEGA’s computational core (MEGA-CC) has undergone extensive refactoring, hardening, and expansion over time. MEGA GUI is now fully cross-platform running natively on Windows, Linux, and macOS. 2011), followed by the incorporation of web technologies to ensure a consistent use-and-feel across Microsoft Windows and Linux operating systems ( Kumar et al. It was then redesigned to become activity-driven ( Tamura et al. 1993) to a rich graphical user interface (GUI) for Microsoft Windows operating system ( Kumar et al. MEGA’s interface evolved from its initial MS-DOS character-based format ( Kumar et al. With every new version, MEGA has evolved to harness technological innovations and personal desktops' computational power. MEGA now contains methods for selecting the best-fit substitution model(s), estimating evolutionary distances and divergence times, reconstructing phylogenies, predicting ancestral sequences, testing for selection, and diagnosing disease mutations ( Caspermeyer 2018). Afterward, the maximum likelihood (ML) methods and Bayesian methods were added for molecular evolutionary analyses ( Tamura et al. ![]() ![]() The data acquisition and integration of major approaches for aligning sequences were introduced to expand MEGA's scope ( Kumar et al. Initially, MEGA contained distance-based and maximum parsimony methods for molecular phylogenetic analysis ( Kumar et al. For more than 25 years, MEGA’s scope and usefulness have grown through the addition of new methods, tools, and interfaces, resulting in modern integrated software for comparative sequence analysis ( Caspermeyer 2018). It was first released in 1993 to offer the statistical methods of molecular evolution through an interactive interface on the Microsoft Disk Operating System (MS-DOS) ( Kumar et al. The Molecular Evolutionary Genetics Analysis (MEGA) software has continuously grown to meet the need for sophisticated evolutionary analysis to discover organismal and genome evolutionary patterns and processes. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from software, phylogenetics, timetrees, tip dating, neutrality Introduction These enhancements will improve the user experience, quality of results, and the pace of biological discovery. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution.
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