Molecular Evolutionary Genetics Analysis MEGA Software for Bioinformatics

Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees.

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Molecular Evolutionary Genetics AnalysisMEGA Software

Molecular Evolutionary Genetics Analysis -  Mega Software

MEGA is a Computer software

Description of MEGA Software

Molecular Evolutionary Genetics Analysis is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees.

It includes many sophisticated methods and tools for phylogenomics and phylomedicine. It is licensed as proprietary freeware. 

Download MEGA Software

Direct Download Link
Home (megasoftware.net)

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Sequence Analyses in MEGA Software

  • Phylogeny Inference
  • Model Selection
  • Dating and Clocks
  • Ancestral States
  • Selection and Tests
  • Sequence Alignment

Statistical Methods in MEGA Software

  • Maximum Likelihood
  • Distance Methods
  • Ordinary Least Squares
  • Maximum Parsimony
  • Composite Likelihood
  • Bayesian

Powerful Visual Tools in MEGA Software

  • Alignment/Trace Editor
  • Tree Explorer
  • Data Explorers
  • Legend Generator
  • Gene Duplication Wizard
  • Timetree Wizard

How to use MEGA software for evolutionary studies of HSP

The video about how to perform evolutionary genetic analysis of heat shock protein and comparative analysis using MEGA software

.Presented about inducing thermotolerance in banana by induction of hsp gene from ideal model sequence. HSPgene has major role in control of heat stress.

Here Brassica juncea species and Musa acuminata species have more similarity when compared to other species since this is taken as template gene for thermotolerance induction.

To compare the similarity i compute the substitution matrix ,pairwise distances,phylogeny tree construction,find gene duplications and find evolutionary probability among that species.

MEGA Guide for First Time Users

MEGAX-Help (megasoftware.net)

Which versions of MEGA are compatible with my macOS system?

Starting in macOS version 10.15 (Catalina), Apple has dropped support for 32-bit applications. For macOS 10.15 and all versions moving forward, MEGAX 10.1.4 and later must be used. However, earlier versions of MEGA can be ran on macOS 10.15 and later by using a Windows version of MEGA with virtualization software such as VMWareFusion.
For the following versions of macOS it is recommended to use MEGAX 10.0.0 or later:
macOS 10.14 (Mojave)
macOS 10.13 (High Sierra)

MEGAX has not been tested on the following versions of macOS. Although MEGA7 has been tested on these versions, support is no longer provided for MEGA7:
macOS 10.12 (Sierra)
macOS 10.11 (El Capitan)
macOS 10.10 (Yosemite)
macOS 10.9 (Mavericks)

If there is not a version of MEGA listed here that is compatible with your macOS system, any of the Windows versions of MEGA can be ran on macOS by using virtualization software such as VMWareFusion.

My mac upgraded macOS system to version 10.15 (Catalina) or newer and now MEGA does not run. What should I do?

Starting in version 10.1.4, MEGAX has been updated to meet the more stringent requirements for running 3rd party applications that were introduced in macOS 10.15 (Catalina). You should download and install MEGAX 10.1.4 or later.

How do I use MEGA-CC?

For basic instructions on using MEGA-CC, see the MEGA-CC-Quick-Start-Tutorial

Do I need to purchase a license to use MEGA?

No. MEGA is provided free of charge for all research and educational purposes. However, it is not permissible to redistribute MEGA in any form to other users. We require that all users download their own copy of MEGA from our website directly. MEGA is protected by all applicable copyright laws.
Download End User Agreement

Can I install MEGA in a classroom/lab using a script?

Because MEGA includes many statistical methods for the study of molecular evolution in an interactive framework, it is instructive for classroom teaching. If you are interested in using MEGA in the classroom/lab, there are no restrictions.
Your students may download a copy from the website www.megasoftware.net or you may install copies on multiple computers in a common computing area.
However, if you want to use MEGA in any other form, please contact the authors by e-mail ( [email protected] ).
If you are using MEGA in classroom teaching, please send us the following information by e-mail for our records ( [email protected] ).

1. Your name, position and institution
2. Course number and title
3. Number of students
4. Course semester and year

To perform a silent install of MEGA on MS Windows computers, call the installer executable with the /SILENT and /VERYSILENT switches.
For example:
MEGA*_setup.exe /SILENT /VERYSILENT

Then MEGA will be installed using the default options. The install will also probably need to be run with admin privileges so that the User Account prompt is not shown.

To perform a silent install of MEGA X on Linux systems, refer to the documentation for the package management software that you are using (probably either dpkg or rpm).

I am not a member of an educational institution. May I still use MEGA?

Yes, MEGA is provided free of charge for commercial institutions as well. However, it is not permissible to redistribute MEGA in any form to other users. We require that all users download their own copy of MEGA from our website directly. MEGA is protected by all applicable copyright laws.

How do I cite MEGA?

Citation for MEGA X:
MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms.
Kumar S, Stecher G, Li M, Knyaz C, and Tamura K (2018)
Molecular Biology and Evolution 35: 1547-1549.
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If using MEGA X on macOS, please cite this paper as well:
Molecular Evolutionary Genetics Analysis (MEGA) for macOS.
Stecher G, Tamura K, and Kumar S (2020)
Molecular Biology and Evolution (accepted).
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Citation for MEGA 7:
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets.
Kumar S, Stecher G, and Tamura K (2016)
Molecular Biology and Evolution 33(7):1870-1874.
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Citation for MEGA 6:
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, and Kumar S (2013)
Molecular Biology and Evolution 30: 2725-2729.
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Citation for MEGA 5:
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
Molecular Biology and Evolution 28: 2731-2739.
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Citation for MEGA-CC:
MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis.
Kumar S, Stecher G, Peterson D, and Tamura K (2012)
Bioinformatics 28:2685-2686.
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Citation for MEGA 4:
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M & Kumar S (2007)
Molecular Biology and Evolution 24: 1596-1599.
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How can I contact the authors, to improve MEGA?

The authors of MEGA appreciate all forms of user suggestions and feedback. In order to properly address each suggestion, we encourage the use of the Suggestion Box form found in the Support/Feedback section of the MEGA website.

I discovered a software bug in MEGA. What should I do?

Please report the bug to the MEGA development team immediately using the Bug Report submission form on the MEGA website. User-submitted bug reports are invaluable to the MEGA development team. Due to limited resources, you may not receive a reply to your bug report immediately, but we can assure you that each bug report will be addressed and responded to as soon as possible by a member of the MEGA development team.

Can I use MEGA in a shared (Terminal Server) environment?

Yes, starting in version 4, we have built support for a multi-user environment, which will allow each user of the same computer to keep his/her customized settings, including file locations, window sizes, choice of genetic code table, and previously-used analysis options. This feature will facilitate educational and laboratory usage where a single computer is often shared by multiple users.

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