MOLECULAR EVOLUTIONARY
GENETICS ANALYSIS
Authors: Koichiro Tamura, Glen Stecher, Daniel Peterson, and Sudhir Kumar
Version 6.0.5
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Update History

note: Some bug fixes are too minor to mention in the change list, and thus have been omitted.

(February 2014) MEGA6.06 update Build 6140219

    Bug fixes

  • Fixed a bug in Alignment Explorer that would cause an access violation when editing the name of a blank sequence
  • Updated the progress dialog for bootstrap to remove flickering and improve efficiency
  • Fixed a bug in Distance Matrix Explorer where export of group calculations would fail if distance data was used
  • Added download progress for the update system
  • Fix for estimation of parsimony branch lengths when ambiguous data is present
  • Updated the integrated browser to remove the cache folder that gets created on start up
  • Removed the email option for sending bug reports (the email account is disabled due to spam)

(January 2014) MEGA6.06 update Build 6140122

    Bug fixes

  • Updated the session system to open .mas files (alignment sessions) made in previous versions of MEGA (retrieves sequence data only)
  • Updated the session system to open .msdx files (data sessions) made in previous versions of MEGA
  • Fixed export of distance matrices for distances computed between groups from the Distance Data Explorer window
  • Turned off bird's eye view in Sequence Data Explorer for short alignments (was causing rendering issues)

(January 2014) MEGA6.05 update Build 6140115

    Bug fixes

  • Fixed a bug in Alignment Explorer where translating then un-translating a segment of data would lose data
  • Fixed a bug in Alignment Explorer where the last site of a sequence would be displayed as a gap character
  • Updated Alignment Explorer to use darker text for highlighted cells making them readable on Windows 7+
  • Fixed one-off error for cut/copy operations in the Alignment Explorer
  • Added missing resource files

(December 2013) MEGA 6.05 Full Release Build 6131211

Features

  • Added an option to open links in new tabs or new windows when using the integrated browser

Fixes

  • Fixed rendering of node height error bars
  • Fixed a bug where a bootstrap value would disappear when re-rooting a tree
  • Fixed memory leak during likelihood calculation

(November 2013) MEGA 6.0 Beta 4 Build 6131127

Fixes

  • Fixed a division by zero error for timetree analysis which would produce a message saying "NAN is not a valid floating point number"

(November 2013) MEGA 6.0 Beta 3 Build 6131108

Fixes

  • Fixed the web browser to open new pages in a new tab instead of a new window when 'target="_blank"'
  • Fixed a bug where drag/drop of fasta files on the main form was not working
  • Fixed caption error where if molecular clock was assumed for ML user tree analysis, the assumption of molecular clock was not mentioned
  • Updated the installer to correctly remove all auxiliary files on un-install

(October 2013) MEGA 6.0 Beta 2 Build 6131022

Fixes

  • The installer in MEGA 6.0 Beta 1 didn't register dlls for image magick.

(October 2013) MEGA 6.0 Beta 1 Build 6131017

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)

(June 2013) MEGA-CC version 5.2.2 Build 5130613

Bug Fixes

  • Fixed a bug where parsing of unaligned Fasta files sometimes failed.
  • Updated HyPhy executable to the version 2.1.2. which includes numerous bug fixes, HBL feature adjustments, and stability improvements

(June 2013) MEGA version 5.2.2 BUILD 5130611

Bug Fixes

  • Fixed caption bug where caption occasionally showed up completely blank.
  • Updated web-browser

(May 2013) MEGA version 5.2.1 BUILD 5130517

Bug Fixes

  • OLE Error in MUSCLE during alignment for MAC Fixed.
  • Updated HyPhy executable to the version 2.1.2. which includes numerous bug fixes, HBL feature adjustments, and stability improvements

(April 2013) MEGA version 5.2 full version released. BUILD 5130424

Bug Fixes

  • Fixed bug in HyPhy related calculations persuant to gap handling.

(October 2012) MEGA version 5.10 full version released.

Bug Fixes

  • Fixed a bug in the installer that allowed multiple instances of MEGA.
  • Updated the installer so it will correctly remove previously installed beta versions.

(May 2012) MEGA version 5.10 Beta update released.

New Features

  • Sped up ML bootstrap tree construction (by avoiding likelihood computation at non-resampled sites).
  • Added TBR (Tree Bisection Reconnection) and SPR (Subtree Pruning Regrafting) search heuristics for MP phylogeny reconstruction.
  • Removed CNI (Close Neighbor Interchange) search heuristic from MP phylogeny reconstruction.
  • Replaced slow TIFF image export with PNG export (similar format, lossless, widely used).

Bug Fixes

  • Fixed a critical calculation bug which occurred in some cases where bootstrapping wasn't resampled correctly (only was an issue with ML trees). This bug only ever existed in the beta.

(January 2012) MEGA version 5.10 Beta released.

New Features

  • Enhanced Maximum Likelihood tree searching to utilize multiple processors/processing cores.
  • Added Subtree-Pruning-Regrafting (SPR) search heuristic for Maximum Likelihood phylogeny inference.
  • Expanded options for automatic initial tree generation for Maximum Likelihood phylogeny inference to include Maximum Parsimony.
  • Added 'Branch Swap Filter' option to ML analyses which gives the user some control over optimization stringency with respect to branch lengths and likelihood improvements.
  • Replaced IE based browser with a Chromium based browser.

Bug Fixes

  • Bug fix for Excel export of results from HyPhy analysis where p-values were reported for codons that were not applicable.
  • Fixed a division by zero error for some datasets when performing Maximum Likelihood 'Test Molecular Clock (ML)'.
  • Fixed a bug where caption expert displays 'Data Specific model' instead of 'General Time Reversible model' for ML inference using GTR.
  • Fixed the Analysis-->User Tree Computation-->Edit/DrawTree (Manually) menu item which was not linked to an event handler.
  • Fixed the Analysis-->User Tree Computation-->Display Newick Tree menu item which also was not linked to an event handler.
  • Fixed an access violation that occurs when displaying CaptionExpert for analysis of a user tree where assume molecular clock == true.
  • Fixed a caption expert bug for Gamma Paramater estimation where the caption incorrectly indicates the source of starting tree.
  • Fixed a bug that occurs when searching for a taxon in Tree Explorer so that MEGA will now jump to the taxon if found and if it is not visible in the current window.
  • Fixed the search function in Tree Explorer so that all matches of the search query will be highlighted.
  • Added a more graceful exception handling for malformed phylip sequence files.
  • Fixed a bug that prevented opening valid phylip sequence files using the Alignment Editor.
  • Fixed a bug where previously, if MEGA couldn't read a MEG file for reasons such as a locked file or one located on a network drive MEGA would crash instead of notifying the user of the problem.
  • Fixed a bug in the App Options Dialog which wasn't correctly enforcing minimum and maximum constraints for values that are keyed in (rather than using the spinners).
  • Fixed bug where site labels were 1 column off in Tree Explorer.
  • For the App Options Dialog used with MUSCLE, removed the confusing checkboxes and updated the default values to reflect what they should be, as recommended by MUSCLE's author.
  • For the App Options Dialog used with MUSCLE, added a 'Restore Defaults' button to restore the default values.
  • Fixed MUSCLE alignment issue by accounting for sequences which may re-order themselves after alignment. This bug would result in sequence data with the wrong name attached to it.
  • Fixed a bug with MUSCLE alignment where the removal of sequences using Alignment Explorer were not handled properly.
  • Fixed ML export of most probable ancestral sequences where indels were not represented correctly.
  • Fixed ML/MP export of ancestral sequence changes list where indels were not represented correctly.
  • Fixed crash bug that would occur when trying to display the caption for NJ trees generated from distance data.
  • Fixed export of caption for model selection where table values had no whitespace between them.
  • Fixed caption for ME phylogeny inference where the caption always reported the search level used as zero.
  • Fixed out of memory crash bug for ML and MP inference. Now if we run out of memory, the user will be notified the analysis is not possible.
  • Fixed sporadic floating point overflow error in ML phylogeny inference.
  • Fixed crash bug that would occur when closing the text editor after converting very large sequence data files to the Mega format.
  • Fixed overflow that would occur when displaying trees with very long taxa names.
  • Fixed overflow error caused by alignments whose length is less than the number of sequences in the alignment.
  • Fixed the calculation of number of degrees of freedom used for molecular clock test.
  • Fixed a bug where dialogs could become hidded behind various explorer windows if the user switches between applications.
  • Fixed rare 'GammaQ' crash bug that could occur when doing linearization.

(April 2011) MEGA Version 5.05 Released

This release was pushed out mainly due to the muscle re-ordering bug, which was fixed in this release. If you are using 5.04 please upgrade ASAP.

Bug Fixes

  • Added additional information for automatic update system and fixed small bug.
  • Simplified MUSCLE interface (removed checkboxes), updated default values based on MSUCLEs suggestoins.
  • Fixed MUSCLE alignment re-ordering bug which was introduced in 5.04 which lead to sequences being associated with the wrong sequence name.
  • Updated citations for Caption Expert.

(April 2011) MEGA Version 5.04 Released

New Features

  • Added option to turn off hiding of overlapping taxa. This is available from the View menu of the Tree Explorer.

Bug Fixes

  • Fixed 'Export Most Probable' option where an error happened if you had selected all ancestors rather than 'Show most probable'.
  • Fixed functions which grabbed sequences via the 'add to alignment' function.
  • Fixed issue with the Tree Builder/Editor dialog where the scrollbar would be very wide, obscuring part of the tree.
  • Removed -stable flag when using Muscle to align sequences upon the author's notification that the flag can cause an unknown bug, refactored MEGA to handle reordering of sequences.
  • Fixed 2 problems in the .mts file. One in the generation of concensus trees, and another in the tree display.
  • Added a progress dialog while downloading updates.
  • Fixed export status message when exporting CSV, text, or MEGA format in the display matrix window.
  • Fixed disappearing output type combo box in display matrix window, and added additional warnings if data is too large.
  • Fixed Composition Distance analysis (previously displayed all 0s).
  • Fixed Disparity Index analysis (previously displayed all 0s).
  • Fixed Disparity Index Test analysis (previously displayed all 0s).

(March 2011) MEGA Version 5.03 Released

Bug Fixes

  • Fixed bug which was accidently introduced only in 5.02 that effected linearization of trees.
  • Fixed issue where some fringe datasets would cause slight linearization score drifts.
  • Fixed some sequence importing from web browser.
  • Introduced new MEGA for the mac system with improved reliability and addressed mac install issues.
  • Released a Linux version for the first time since MEGA 4.0.

(February 2011) MEGA Version 5.02 Released

Bug Fixes

  • Fixed tie tree problem.
  • Fix for bug #0002672 Subject: Overwriting of sequences with duplicate names in fasta input.
  • Fix for the number of parameters reported for JC in Best DNA/Protein Models

(January 2011) MEGA Version 5.01 Released

Bug Fixes

  • Improved the initial tree making method for ML (now chooses between NJ and BioNJ trees based on superior likelihood)
  • User Tree branch length corrected
  • Bug fix to ignore user tree branch lengths
  • Display fix for HyPhy output
(2011) MEGA Version 5.0 Released
(2010) MEGA Version 5.0 Beta Released
(2008) MEGA Version 4.1 Released
(2006) MEGA Version 4.0 Released
(2004) MEGA Version 3.0 Released
(2001) MEGA Version 2.1 Released
(2000) MEGA Version 2.0 Released
(1994) MEGA Version 1.1 Released
(1993) MEGA Version 1.0 Released
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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

  NEW! Online Manual NEW!
Reference and documentation.
  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 6 Downloads:
MEGA 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.
- Download PDF

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.
- Download PDF

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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