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Short answer: MEGA X is version 10 of MEGA (Molecular Evolutionary Genetics Analysis), a free desktop program for aligning DNA and protein sequences, inferring phylogenetic trees, estimating genetic distances and testing for selection. It was described in Molecular Biology and Evolution in 2018 and ran natively on Windows and Linux, with a graphical interface and a command-line companion, MEGA-CC. MEGA 11 and MEGA 12 have since replaced it as the current release, so the version you cite should be the version you actually ran. This is not the Mega.nz cloud-storage service, which shares only the name.
What MEGA X is
MEGA is a long-running software series for comparative analysis of molecular sequences. The MEGA X paper (Kumar, Stecher, Li, Knyaz and Tamura, Molecular Biology and Evolution 2018;35(6):1547-1549, doi:10.1093/molbev/msy096) lists its core functions: sequence alignment, phylogenetic tree inference, genetic distance and diversity estimation, ancestral sequence inference, timetree construction and tests of selection. “MEGA software” in a search therefore usually means the whole series, and “MEGA X” means the 10.x releases from 2018 to 2021. The software is distributed free of charge from megasoftware.net (read 2026-11-08).
How MEGA X is used in practice
Graphical interface and MEGA-CC
According to the MEGA X paper, the program has a graphical interface with an ANALYZE mode and a PROTOTYPE mode, and a separate command-line version, MEGA-CC. Settings chosen in the graphical interface can be saved with “Save Settings” as a file that MEGA-CC then reads, so an analysis configured once by hand can be repeated unattended on another machine or on a batch of datasets. The earlier Mega-Proto tool is no longer supported.
Operating systems and compute
The paper reports native builds for 64-bit Windows (with a 32-bit option) and for Debian/Ubuntu and RedHat/CentOS-based Linux, tested on Ubuntu 16.04.4, Linux Mint 18.1 and CentOS 7, without virtualization or emulation. macOS support was still in development when the paper was written; the official version history lists a native 64-bit macOS beta in MEGA 10.1.0 (June 2019). By default, MEGA X uses all available processor cores minus one; the maximum can be set under Analysis Preferences. Model selection and bootstrap tests for distance and parsimony methods are parallelized.
For a step-by-step tree-building protocol, see the CASRAI guide Make a Phylogenetic Tree; to read the output, see How to Read a Phylogenetic Tree.
MEGA X compared with MEGA 11 and MEGA 12
The table below is taken from the official MEGA version history (megasoftware.net/history, read 2026-11-08) and the MEGA11 paper (Tamura, Stecher and Kumar, Mol Biol Evol 2021;38(7):3022-3027, doi:10.1093/molbev/msab120). It lists changes the sources themselves name; it is not a performance comparison.
| Release line | Dates on the history page | Changes the sources name |
|---|---|---|
| MEGA X (10.0 to 10.2) | February 2018 to May 2021 | 10.0.0: graphical interface native on Linux and Windows, alignment concatenation, .ods/.xlsx export. 10.0.1: Prototype mode, MEGA-CC distributed with MEGA. 10.0.4: evolutionary probabilities and codon-by-codon selection (SLAC). 10.1.0: native 64-bit macOS build without WINE; RTDT and calibration densities. 10.2.x: explorer and calibration refinements. |
| MEGA 11 (11.0.x) | January 2021 to June 2022 | Full dates in RTDT, more memory-efficient maximum likelihood, redesigned Tree Explorer toolbar; the MEGA11 paper also reports probability-density calibrations and tip-dating, on native Windows, Linux and macOS with GUI and command line. |
| MEGA 12 (12.0.x to 12.1) | December 2024 to October 2025 | Filter-based model selection, adaptive bootstrap, DrPhylo, a Poisson amino-acid model; macOS Intel and M-series and 64-bit Linux builds; in 12.1.0, a Calibration Editor connected to the TimeTree API and session files that work across operating systems. |
The MEGA home page lists MEGA 12.1 as the current release for Windows, macOS and Linux, with older versions still available for download.
Where the version matters in a lab
- Reproducibility. Cite the release you actually used: the MEGA X paper for 10.x, the MEGA11 paper for 11.x, and the MEGA 12.1 article (doi:10.1007/s00239-025-10287-z) for 12.1. Record the full version number in your methods or lab notebook, since model-selection and bootstrap options differ between lines.
- Unattended runs. If the analysis is scripted through MEGA-CC, keep the settings file with the data so the run can be repeated.
- Shared compute. Because the default is all cores minus one, set the core limit in Analysis Preferences before running on a shared workstation or server.
- Tool choice. For large maximum-likelihood datasets, see IQ-TREE; for choosing an aligner first, see MAFFT vs MUSCLE vs Clustal Omega vs T-Coffee.
Common misunderstandings
- MEGA X is not a separate program from MEGA. It is one release line of the same series.
- MEGA is not Mega.nz. The cloud-storage service has no connection to the phylogenetics software beyond the name.
- MEGA X is not the latest version. The official site now lists MEGA 12.1.
- The graphical interface is not the only interface. MEGA-CC runs analyses from the command line.
FAQ
What is MEGA software?
MEGA (Molecular Evolutionary Genetics Analysis) is a free program for sequence alignment, phylogenetic tree inference, distance estimation and selection tests, distributed from megasoftware.net.
Is MEGA X free?
Yes. The MEGA X paper states it is free of charge, and the official site states no price. Use is subject to the End User Agreement linked from the site.
Which operating systems does MEGA X run on?
Per the 2018 paper, 64-bit and 32-bit Windows and several Linux distributions natively; the version history adds a native macOS build from 10.1.0.
Which MEGA paper should I cite?
The one matching the version you ran: the 2018 MEGA X paper for 10.x, the 2021 MEGA11 paper for 11.x, or the MEGA 12.1 article for 12.1.
Sources
- Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018;35(6):1547-1549. PMC5967553 (read 2026-11-08).
- Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021;38(7):3022-3027. PMC8233496.
- MEGA Software, home page and version history (read 2026-11-08).
- Related: Molecular Biology and Evolution journal (publisher of the MEGA papers).
