7 versions of MEGA12 (CLI) are listed here, from April 9, 2025 to the current 12.1.4. Each one links to the publisher’s own installer files.
7 versions over 2 years · about 4.5 a year
| Version | Date | Size | Files |
|---|---|---|---|
| 12.1.4Latest | October 23, 2026 | 215.1 MB | 64-bit EXE (Inno Setup) 203.0 MB32-bit EXE (Inno Setup) 215.1 MB Release notesBug Fixes
- Fixes an error when cancelling ML tree construction with bootstrap where Tree Explorer would display the topology from the last completed replicate. |
| 12.1.3 | October 2, 2026 | 215.1 MB | 64-bit EXE (Inno Setup) 203.0 MB32-bit EXE (Inno Setup) 215.1 MB Release notesBug Fixes
- Name and divergence time searches using the Timetree resource have been updated to use the new Timetree API URLs.
- Distance calculations using the Pamilo-Bianchi-Li and Li-Wu-Luo methods for dN and dS estimation on Windows operating systems have been fixed.
- Scale bar positioning for trees displayed in the radial style has been updated to avoid overlapping with taxa names.
- Missing citation for MEGA 12.1 on Linux operating systems has been fixed. |
| 12.1.2 | December 16, 2025 | — | 64-bit EXE (Inno Setup)32-bit EXE (Inno Setup) Release notesUpdates
- The installers for Windows operating systems are now code-signed.
Bug Fixes
- Ancestral sequence inference when using the UCSC 46-species tree has been updated to maintain the correct tree rooting. This is part of the mutation diagnosis analysis.
- Fixed size and positioning of components when using the Calibration Editor on high dpi monitors.
- Refactored naive mapping of taxa groups that was sluggish for very large data.
- Fixed an access violation when using the prototyper to generate a .mao file for Reltime with branch lengths. |
| 12.1.1 | November 19, 2025 | — | 64-bit EXE (Inno Setup)32-bit EXE (Inno Setup) |
| 12.0.15 | October 23, 2025 | — | 64-bit EXE (Inno Setup)32-bit EXE (Inno Setup) |
| 12.0.14 | August 20, 2025 | — | 64-bit EXE (Inno Setup)32-bit EXE (Inno Setup) Release notesBug Fixes
- Fixes an access violation in the Calibration Editor when overwriting an existing calibration.
- Fixes a memory leak in Maximum Likelihood tree construction with bootstrap.
- On Linux, fixes an incorrect count of the number of processors available.
- For the position-by-position rates analysis, use the number of threads specified by the user.
- Fixes an error in the Sequence Data Explorer where the genes/domains popup menu was displayed along with groups popup menu.
- Fixes incorrect row mapping for the groups context menu in the Sequence Data Explorer.
- Fixes false detection of user cancellation for very small data when doing Maximum Likelihood tree construction. |
| 12.0.11 | April 9, 2025 | — | 64-bit EXE (Inno Setup)32-bit EXE (Inno Setup) Release notesBug Fixes
- Fixes the path to the MUSCLE executable for the 32-bit version of MEGA12.
- When exporting trees to Newick files, always use the period character regardless of locale.
- Updates the URL for DrPhylo help to use the correct github branch.
- Fixes a "list index out of bounds" error when sorting groupwise distance matrix results.
- Synchronizes threads for the Mutation Diagnosis tool. |