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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Test of Positive Selection

In this example, we present various analyses of protein-coding nucleotide sequences for five alleles from the human HLA-A locus (Nei and Hughes 1991).

Ex 6.0.1 Start MEGA by double-clicking on the MEGA desktop icon, or by using the Windows start-menu to click on the MEGA icon located in the programs folder.

Ex 6.1.1 Activate the data present in the HLA_3Seq.meg file by using the File|Open command.

Ex 6.1.2 Now that the data file is active, note that various details about the data file are displayed at the bottom of the main application window, and more menu items have become available on the main menu.

Let us compute the synonymous and nonsynonymous distances appropriate for studying positive Darwinian selection in this set of antigen recognition codons.

Ex 6.2.1 Select the Selection|Codon-based Z-Tests from the menu command. An analysis preferences dialog appears. Use the Models pull-down in the Options Summary tab to select Syn-Nonsysnonymous|Nei-Gojobori Method|p-distance model. In the Test Hypothesis (HA: alternative) tab, select Positive Selection (HA: dN > dS) from the pull-down, and select the Overall Average from the Analysis Scope tab. Click the GAPS/Missing Data tab and make sure that the Pairwise Deletion option is selected.

Ex 6.2.2 Click on “Compute” to accept the default values for the remaining options. A progress indicator appears briefly; the computation results are displayed in a results window in grid format.

Ex 6.2.3 The Prob column contains the probability computed (must be <0.05 for hypothesis rejection at 5% level), and the Stat column contains the statistic used to compute the probability. The difference in synonymous and nonsynonymous substitutions should be significant at the 5% level.

Ex 6.2.4 Exit MEGA and deactivate the active data file using the Alt + X command.