Genome sequencing is generating vast amounts of DNA sequence data from a wide range of organisms. As a result, gene sequence databases are growing rapidly. In order to conduct efficient analyses of these data, there is a need for easy-to-use computer programs, containing fast computational algorithms and useful statistical methods. The objective of the MEGA software has been to provide tools for exploring, discovering, and analyzing DNA and protein sequences from an evolutionary perspective.
What's new in 12.1.4
Bug Fixes
Fixes an error when cancelling ML tree construction with bootstrap where Tree Explorer would display the topology from the last completed replicate.
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
Updates - 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
Other versions
12.0.15
12.0.14
12.0.11
Frequently asked questions
Is MEGA12 (CLI) free?
MEGA12 (CLI) is proprietary software from iGEM. Check the publisher's license terms for pricing and usage rights.
What is the latest version of MEGA12 (CLI)?
The latest version is 12.1.4, released on Oct 23, 2026.
Is it safe to download MEGA12 (CLI)?
The download button links to the official installer published on megasoftware.net, the same file Windows Package Manager installs. You can verify the downloaded file by comparing its SHA-256 checksum with 11a4ddfd7c578a948ea014ff07c9a1173da24b8fa6b790e2e715f700959034d7.
Which Windows versions does MEGA12 (CLI) support?
MEGA12 (CLI) runs on Windows and is available for 32-bit (x86), 64-bit (x64) systems.
How do I install MEGA12 (CLI) silently?
Run the offline installer with "MEGA_CC_12.1.4_win64_setup.exe" /VERYSILENT /SUPPRESSMSGBOXES /NORESTART /SP-, or install it with Windows Package Manager: winget install --id=iGEM.MEGA.CLI.12 -e --silent.
How do I uninstall MEGA12 (CLI)?
Open Settings › Apps › Installed apps, find MEGA12 (CLI) and select Uninstall. From the command line, run winget uninstall --id=iGEM.MEGA.CLI.12 -e.
What file types can MEGA12 (CLI) open?
MEGA12 (CLI) supports 12 file types, including .fas, .fasta, .fsa, .mas, .masx, .mdsx, .meg, .mts and more.
Alternatives to MEGA12 (CLI)
Other Command Line Tools programs for Windows from different developers.
The Azure command-line interface (Azure CLI) is a set of commands used to create and manage Azure resources. The Azure CLI is available across Azure services and is designed to get you working quickly
