MEGA (Molecular Evolutionary Genetics Analysis) is a free, widely used package for sequence alignment, phylogenetic tree building and molecular evolution analysis. It runs on Windows, macOS and Linux with a point-and-click interface, which makes it a common starting point for phylogenetics.
Download MEGA from the official site ↗
What you can do with MEGA
- Align sequences (built-in ClustalW and MUSCLE).
- Build phylogenetic trees — Neighbor-Joining, Maximum Likelihood, Maximum Parsimony, UPGMA — with bootstrap support.
- Estimate evolutionary distances and test substitution models.
- Analyse selection (dN/dS) and molecular clocks.
Who it’s for
MEGA suits students and researchers who want robust phylogenetics without scripting. For pipeline/automated work, command-line tools (RAxML, IQ-TREE, MAFFT) or R packages are more flexible; MEGA also offers a command-line edition (MEGA-CC) for batch analyses.
Getting started
- Download and install the edition for your operating system from megasoftware.net.
- Import sequences (FASTA) and align them inside MEGA.
- Choose a tree-building method and run it with bootstrap replicates for support values.
Frequently asked questions
Is MEGA free?
Yes, MEGA is free for academic and commercial use, on Windows, macOS and Linux.
Can MEGA align sequences?
Yes — it includes ClustalW and MUSCLE for alignment before tree building.
What tree methods does MEGA support?
Neighbor-Joining, Maximum Likelihood, Maximum Parsimony and UPGMA, with bootstrap and model selection.
