![]() ![]() Such GUIs enhanced the user experience by providing more screen space for displaying larger amounts of data and results, allowed for a more sophisticated and intuitive display of information, and enabled more intuitive and efficient data manipulations. We decided to evolve MEGA's character-based user-interface from a 640 × 480 pixel size screen to a GUI. ![]() In 1995, the release of Microsoft Windows 95 led to the first stable graphical user interface (GUI) for Intel-CPU-based personal computers, which were called IBM compatibles. These first-hand experiences spurred a more widespread appreciation of statistical methods for phylogenetic analysis, which was clearly reflected in the fast-growing citations of the NJ method (over 16 000 citations to date) and software packages, such as MEGA 1, providing access to statistical methods in phylogenetics ( Figure 1 in ). By using the NJ method to infer phylogenetic tree in MEGA, researchers often discovered that the NJ method generated a tree quickly for data sets containing many sequences and that differences between NJ trees and those produced by other time-consuming methods were localized to parts of the trees that were usually statistically weakly supported. A case in point is the application of the Neighbor-Joining (NJ) method in phylogenetic inference. The main MEGA windows are overlaid with the Input Sequence Data Explorer, in which columns containing at least two different types of nucleotides (variable sites) are highlighted.Īvailability of easy-to-use MEGA 1 initiated many biologists to begin exploring the utility of distance-based methods in molecular evolutionary genetic analysis we received hundreds of request for MEGA 1 in the first year of its release. MEGA 1 evolved into a Windows program (MEGA 2) with an extensive GUI ( B). Screenshots of the first version of MEGA containg a character-based point-and-click interface for use on DOS ( A). In addition, facilities were provided to compute basic statistical properties of DNA and protein sequences, and tools were included for the visual exploration of input sequence data and inferred phylogenies. It offered many methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference and statistical tests of inferred phylogenies. In order to make statistical methods available for phylogenetic analysis in a user-friendly manner, we produced a program with character-based mouse/menu interface for use on DOS systems in 1993 ( Figure 2A). ![]() ![]() These programs were (and continue to be) very useful, but the former lacked statistical methods at that time and the latter did not provide a point-and-click user interface. One was PAUP for constructing parsimony trees, and the other was PHYLIP for inferring phylogenetic trees using various character and statistical methods such as maximum likelihood, parsimony and distance methods. There were two primary general-purpose computer programs for inferring phylogenetic trees. At this time, most computer programs available did not allow us to explore the primary data visually and lacked a user-friendly interface. The MEGA software project grew out of our own need for employing statistical methods in the phylogenetic analysis of DNA and protein sequences in the early 1990s. An asterix marks features that are expected to be included in versions 4.1, 4.2, and 5. ![]()
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