Authors: Koichiro Tamura, Glen Stecher, Daniel Peterson, and Sudhir Kumar
Version 6.0.6

MEGA 6 Release Notes

New Features

    MEGA6 contains a number of enhancements over MEGA5. A brief communication (MEGA6: Molecular Evolutionary Genetics Analysis version 6.0) describing the new features in MEGA6 has been published in the journal Molecular Biology and Evolution. A PDF of this brief communication can be downloaded here

  • Added a Timetree system for estimating relative and absolute times of divergence for all branching points in a phylogeny that is based on the Reltime method described in Tamura et al. 2012 and which supports multiple user-defined calibration constraints.
  • Added support for internal node labels in Newick files in order to facilitate mapping of divergence times in MEGA's tabular timetree output. Internal node labels should be placed in single quotes.
  • MEGA's capacity to allocate system memory has been doubled for 64-bit computers by setting the IMAGE_FILE_LARGE_ADDRESS_AWARE bit.
  • The Tree Explorer was enhanced to allow for the display of trees with up to ~4,000 taxa.
  • A bird's eye summary view was added to the Sequence Data Explorer. This view facilitates fast navigation across genes and domains.
  • The LG amino acid model (Le and Gascuel 2008) was added for amino acid and protein-coding data.
  • For Maximum Parsimony phylogeny construction, the CNI search method was replaced by the Subtree-Pruning-Regrafting (SPR) and the Tree-Bisection-Reconnection (TBR) approaches.
  • Support for groups was added to the Alignment Explorer.
  • Added support for exporting to fasta files from the Sequence Data Explorer.
  • Added a utility for displaying node ids in the Tree Explorer (click View | Show/Hide | Node Ids)
  • Added an option to open links in new tabs or new windows when using the integrated browser


  • Tree session files made using previous versions of MEGA cannot be opened in MEGA6. As a workaround, the session files can be opened in the version of MEGA that was used to create the session and the topology can be exported to a .nwk file. Then the exported file can be opened in MEGA6.
  • Alignment session files made using previous versions of MEGA lose some information when opened in MEGA6. Specifically, the settings used for alignment and form state(fonts, colors, etc...) are lost.


Book Book Molecular Evolution and Phylogenetics (2000)
Introductory book containing many examples for use with MEGA.
Book Book Phylogenetic Trees Made Easy (2011) (2007)
A cookbook for learning phylogenetic analysis using MEGA and other programs.
  MEGA: Molecular Evolutionary Genetics Analysis (1993).
Institute of Molecular Evolutionary Genetics. University Park, PA, USA.
  Building Phylogenetic Trees from Molecular Data with MEGA(2013)
A Paper, which explains how to construct phylogenetic trees using MEGA.
  A Walk Through MEGA
Step-by-step instructions to learn how to use MEGA.
  Useful Publications
MEGA related publications.
  MEGA Team
Research and development team.
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Using MEGA

  Online Manual
Reference and documentation.
The basics of using the MEGA-CC command-line version
  MEGA 6 release notes
A list of major changes and new features in the current stable version of MEGA.
  Update History
A comprehensive list of major changes with each software release.
  Report a Bug
Help us improve our software by reporting problems you encounter using MEGA.
  Example Data
The following data files are provided as downloads for reference purposes.
  Suggestion Box
User feedback plays an important role in the development of MEGA.
Frequently asked questions.
  Known Issues
Known issues which exist in MEGA.
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Download Stats

MEGA 7 Downloads:
MEGA-CC 7 Downloads:
MEGA 6 Downloads:
MEGA-CC 6 Downloads:
MEGA 5 Downloads:
MEGA-CC 5 Downloads:
MEGA 4 Downloads:
MEGA 3 Downloads: 106,285
MEGA 2 Downloads: 69,828
MEGA 1 Downloads: 2,929
Contact Us
Email us with any questions or concerns.
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Citing MEGA in a Publication

Citation for MEGA 6:
Tamura K, Stecher G, Peterson D, Filipski A, and Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution 30: 2725-2729.
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Citation for MEGA-CC:
Kumar S, Stecher G, Peterson D, and Tamura K (2012) MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis. Bioinformatics 28:2685-2686.
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Citation for MEGA 5:
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
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Citation for MEGA 4:
Tamura K, Dudley J, Nei M and Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
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Citation for MEGA 3:
Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Briefings in Bioinformatics 5:150-163.
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Citation for MEGA 2:
Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis Software. Bioinformatics 17:1244-1245.
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Citation for MEGA 1:
Kumar S, Tamura K, Nei M. (1994) MEGA: Molecular Evolutionary Genetics Analysis Software for Microcomputers. Computer Applications in Biosciences 10:189-191.
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