MOLECULAR EVOLUTIONARY
GENETICS ANALYSIS
Authors: Koichiro Tamura, Glen Stecher, Daniel Peterson, and Sudhir Kumar
Version 6.0.6
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MEGA 7 Release Notes

New Features

  • MEGA7 is now optimized for 64-bit processors and can utilize a drastically larger amount of RAM. We have successfully tested MEGA with ML analyses using large data sets that required > 40GB of RAM.
  • The Tree Explorer has been re-factored so that it can now display trees with > 100k taxa (dependent on the graphics capabilities and memory available on the host computer)
  • The timetree system has been redesigned to use a wizard-style workflow. The major element of this new system is a Timetree Wizard which walks the user through all of the steps necessary to generate a timetree in MEGA.
  • The timetree system in MEGA now supports the use of an outgroup to properly root the tree. It is now also possible to define an outgroup using the Taxa/Groups dialog.
  • The timetree system now computes data coverage at all internal nodes in a timetree. This is useful for identifying problematic nodes in the tree where divergence time estimates may be unreliable due to insufficient data coverage (see Filipski et al. 2014)
  • A utility for identifying gene duplication events in a gene tree has been added. Additionally, if an optional trusted species tree is provided, then the algorithm described in Zmasek and Eddy 2001 is used to mark all internal nodes in the gene tree as either gene duplication or speciation events.
  • We have added additional image export formats (including the return of the TIFF format)
  • We have removed the dependency on Image Magick for exporting images of trees
  • The integrated web browser has been upgraded from version 1 of the Chromium Embedded Framework to version 3

*** Important Notes ***

  • MEGA7 will not open session files created with earlier versions of MEGA. Although inconvenient, this limitation is necessary for 64-bit optimization of MEGA. To retrieve data from session files made with previous versions of MEGA, users can open the session files with the same version of MEGA that created the session and export the data to .meg or .nwk files as needed. Then the data can be used in MEGA7.
  • MEGA7 is compiled for use only on 64-bit computers (this will apply to future versions as well). Users that wish to run MEGA on 32-bit systems must use MEGA6 or earlier

MEGA-CC 7 Release Notes

New Features

  • MEGA-CC is now optimized for 64-bit processors and can utilize a much larger amount of RAM. We have successfully tested MEGA with ML analyses using large data sets that required > 40GB of RAM.
  • MEGA-CC has been ported to the Lazarus/Free Pascal programming language and is now compiled natively for Windows, Linux, and Mac OS operating systems. It is no longer necessary to use virtualization/emulation software to run MEGA-CC on Unix-based systems.
  • The timetree system in MEGA now supports the use of an outgroup to properly root the tree.
  • The timetree system now computes data coverage at all internal nodes in a timetree. This is useful for identifying problematic nodes in the tree where divergence time estimates may be unreliable due to insufficient data coverage (see Filipski et al. 2014)

*** Important Notes ***

  • MEGA-CC 7 is compiled for use only on 64-bit systems (this will apply to future versions as well). Users that wish to run MEGA-CC on 32-bit systems must use MEGA-CC 6 or earlier

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

Issues

  • 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.
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Resources

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.
  MEGA7-CC-Quick-Start-Tutorial
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.
  FAQ
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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