Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution.
(to be submitted)
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
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Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
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MEGA 4: Molecular Evolutionary Genetics Analysis

MEGA is an integrated tool for conducting automatic and manual sequence alignment,
inferring phylogenetic trees, mining web-based databases, estimating rates
of molecular evolution, and testing evolutionary hypotheses.

MEGA 4 has been tested on the following Microsoft Windows® operating systems:

Windows 95/98, NT, 2000, XP, Vista, and Windows 7.

New Features:

  • Real-Time Caption Expert Engine
    A unique facility to generate detailed captions for different types of analyses and results. These captions are intended to provide detailed, natural language descriptions of the methods and models used in analysis. The facility aims to promote a better understanding of the underlying assumptions used in analysis, and also of the results generated.
  • Maximum Composite Likelihood Method
    A method for estimating evolutionary distances between all pair of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This method can also be used to estimate transition/transversion biases and nucleotide substitution patterns without requiring a priori knowledge of the phylogenetic tree.
  • Linux Version
    This software package is now programmed to run efficiently in the Linux desktop environment on top of Wine, an open-source compatibility layer for running Windows programs on Unix-based Operating Systems.
  • Multi-User and Multi-Threading Support
    The multi-user environment will support each user of the same computer to preserve their customized settings, choice of genetic code table, and a variety of analysis options.


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