MEGA 12 contains new approaches for working with large data as well as a number of enhancements over previous versions. They include:
Filtered best-fit ML model test that skips evaluation of derivative models unlikely to be optimal has been added to MEGA.
Adaptive bootstrap test of phylogeny that automatically determines the number of replicates needed when using the Maximum Likelihood approach has been added to MEGA.
The Maximum Likelihood (ML) framework in MEGA has been further parallelized and optimized for working with long sequence alignments.
For tree construction with the bootstrap test of phylogeny, the Tree Explorer has an option to show a range for bootstrap support.
MEGA is now DPI aware so that the sizing and spacing of components is improved when MEGA is run on systems with ultra high resolution monitors.
The integrated web browser has been updated with current Chromium Embedded Framework libraries.
MEGA 12 includes many improvements to usability (e.g., scrolling improvements for large alignments, improved progress reporting, etc...).
The Tree Explorer now allows one to clone a current session to a new window.
The DrPhylo analysis (see Sharma and Kumar 2024) for assessing the fragility of inferred clades has been added.
Quick navigation to any results window currently open in MEGA can be done through the Windows menu at the top of any other results window.
A note about compatibility between different versions of MEGA
ยท Session files (*.masx, *.mtsx, *mdsx) cannot be shared between different platforms. For example, a tree session file (file.mtsx) created on a Linux or macOS system cannot be opened on a Windows computer. Additionally, a session file generated on a 32-bit operating system should not be opened on a 64-bit system and vice-versa.