Update History
(April 2017) MEGA7.0.25 build 7170412

Updates

  • Changed file extensions for alignment and tree sessions to .masx and .mtsx repectively because Microsoft Windows is now associating the original file extensions (.mas and .mts) with media file formats
  • Allow users to continue user tree analyses from the Topology Editor without forcing all sequences to be used or all tree taxa to be resolved
  • Allow users to cancel long-running SPR and TBR parsimony bootstrap tree construction part of the way through and use only the reps completed as long as the min number of reps (50) have finished
  • Added divergence time confidence intervals when Reltime is performed on trees generated using distance or parsimony methods

Bug Fixes

  • Fixed memory leak when doing ML tree construction with bootstrap
  • Bug fix for importing outgroup taxa names in TaxaGroupsDlg when doing the Reltime analysis
  • Fixed potential division by zero error in Reltime
  • Fixed bug where exporting captions as text would produce an empty result
  • For ML analyses, validate that sufficient data is available for executing the calculation
(November 2016) MEGA7.0.21 build 7161102

Updates

  • Added Nexus export of Reltime trees
  • Optimized the Reltime variance estimation
  • The Windows installer for MEGA-GUI now has an option to remove older versions
  • Added progress updates for saving alignment sessions
  • Updated the Tree Explorer to support taxa name editing

Bug Fixes

  • Fixed a bug in the Applinker where the MUSCLE process would not terminate properly if the user aborted the alignment
  • Handle the case where a user closes the active data file while phylogeny construction is still running
  • Bug fix for ML tree construction where if the user cancelled the analysis, the calculation still went to completion
  • Bug fix for the Alignment Editor where if trying to remove gaps fails, the editor was not re-enabled
  • Fixes a list index out of bounds error when doing alignment with a blank sequence
  • Do not allow users to open or add new data in Alignment Explorer while a sequence alignment is in progress
  • Improved the warning message that is displayed when MUSCLE removes sequences - now only shows 1 message instead of multiple
(January 2016) MEGA7.0.14 build 7160126

Updates

  • Reltime CI estimation has been improved for the deepest node
  • Reltime calibrations are now saved in tree session files
(January 2016) MEGA7.0.13 build 7160122

Updates

  • After running the Reltime analysis, it is now possible to recalibrate the timetree without running the Reltime calcuation anew
(January 2016) MEGA7.0.11 build 7160105

Bug Fixes

  • Updated Alignment Explorer so that launching a BLAST search on NCBI correctly populates the input form
  • Added a 'shutdown gracefully' thread that waits for any CEF browser threads to terminate before the main form closes to avoid potentially orphaned CEF browser threads
(November 2016) MEGA7.0.7 build 7151112

Bug Fixes

  • Fixed one-off error in Alignment Explorer when translating selected sites
(October 2016) MEGA7.0.5 build 7151012

Updates

  • Added drag/drop support to the text editor
  • Added a button to the text editor to make closing individual tabs more intuitive
(August 2015) MEGA7.0.3 beta build 7150818

Bug Fixes

  • Improved the calculation of standard error for divergence times for the Reltime method
  • Fixed a bug in Analyze User Tree by Maximum Likelihood where the calculated log likelihood value could be incorrect for some datasets (although branch lengths are still correct)
  • Disallowed opening of tree session files made in MEGA6.06
  • Fixed a bug in the Taxa/Groups window where the icons for disabled buttons were not visible
  • Added auto-pruning of any unused taxa from the user tree for the Reltime method
  • Updates to the help documentation
  • Fixed one-off errors in exports of ancestral sequences to Excel and CSV files
(June 2015) MEGA7.0.0 beta build 7150624

New Features

  • MEGA7 is now optimized for 64-bit processors and can utilize a drastically larger amount of RAM
  • The Tree Explorer has been refactored so that it can now display trees with > 100k taxa (dependent on the graphics capabilities and memory available on the host computer)
  • Added a Timetree Wizard that simplifies the creation of timetrees
  • Added support for rooting a timetree on an outgroup
  • The timetree system now computes data coverage at all internal nodes in a timetree
  • Added additional image export formats (including the return of the TIFF format)
  • Removed the dependency on Image Magick
  • Updated the Taxa/Groups dialog to support the definition of outgroups
  • Updgraded the integrated browser 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 in order to compile MEGA with 64-bit optimization. To retrieve data from session files made with previous versions of MEGA, 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 (and future versions of MEGA) is compiled for use only on 64-bit computers. Users that wish to run MEGA on 32-bit systems must use MEGA6 or earlier

Bug Fixes

  • Fixed a bug in the text editor where the horizontal scrollbar would only scroll to 1024 characters
  • Fixed a bug where unrooted trees exported to a Newick file would be rooted
  • Moved the Examples folder from the Program Files folder (which can lead to access control issues) to the user's Documents directory
  • Fixed one-off errors in the Sequence Data Explorer and Alignment Explorer where the last site in an alignment was sometimes not displayed
  • Fixed typecast error when exporting results from the Caption Expert to Excel or csv files
(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

New Features

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

Bug 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

Bug 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

Bug 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

Bug 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.
(May 2012) MEGA version 5.10 Beta update released.

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 5.05 Released

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
Older Releases
(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