Update History

(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

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