Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
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Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
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Known Limitions

  • MEGA 4 Linux - "Unable to write to z:\\...\MEGA\private\Ini\MEGA40state.ini" Solution: Chmod the folder to allow write access
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  • MEGA 4.1 Beta - Opening MEGA associated files by double clicking does not work. Solution: Upgrade to MEGA 4.1 Beta 3

  • MEGA 4.X - Saving tree as TIFF image produces error 'Access violation at Address 00742610 in Module "MEGA4.exe"' Solution: Adjust your monitor Color Quality to 32-bit

  • MEGA 4.X - Saving a large tree as TIFF image produces error "Not enough storage is available to process this command" Solution: Make the tree smaller by lowering 'Taxa Seperation' and 'Tree Width' to make the tree smaller and try again. TreeExplorer->View->Options->Tree Tab

  • MEGA 3.X/4.X - Show Subtree Separately doesn't work and shows the entire tree. Solution: This issue only occurs when opening a newick file by double clicking on it. Instead, open the newick file from the main menu. MEGA Main Menu->Phylogeny->Display Newick Trees from File

  • Problem to read PAUP/Nexus format sequence smoothly.

  • Error when attempting to blast a sequence ("can't move focus to the control because it is invisible, not enabled, or of a type that does not accept the focus"). Solution: Upgrade to MEGA 4.1 Beta 3

  • Sorting distance data by name/group name does not work