Molecular Evolutionary Genetics Analysis (MEGA) software contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this talk, the focus will be on major new developments that will enable researchers to use MEGA for (a) phylogenetic inference of very large datasets, (b) building very large timetrees quickly and accurately using innovative methods, (c) automatically predicting gene duplication events in gene family trees, and (d) conducting high-throughput and scripted analyses using a computational core. The new MEGA software suite is now 64-bit and is available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command line computational core MEGA-CC is available as native applications for Windows, Linux, and Mac OSX. All MEGA versions are available from www.megasoftware.net free of charge.