Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution.
(to be submitted)
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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Introduction to Walk Through MEGA

This section provides a MEGA tutorial. The data files for these examples can be found in the EXAMPLES folder, located in the MEGA installation directory (example in C:\Program Files\MEGA3\Examples). In these example files, data are deliberately written in different input formats. We recommend that you study the examples in the order presented because the techniques explained in the initial examples are used again in the subsequent ones.

In the following write-up, highlighted words indicate the keys you must press on the keyboard. If you must press two keys simultaneously, they are shown with a + sign between them (e.g., Alt + F3 means that the Alt and F3 keys should be pressed simultaneously). Italicized letters are used to mark the commands found in menus, submenus, and other locations as they appear on the computer screen. In every example, we discuss many procedures introducing analytical techniques. For ease of reference in later examples, these procedures are numbered in the Ex u.v.w format, where u is the example number, v is the procedure number, and w is the step number. For instance, Ex 1.3.2 refers to the 2nd step of the 3rd procedure in example 1.