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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Estimating Evolutionary Distances from Nucleotide Sequences

In this example, we will compute various distances for the Adh sequences from 11 Drosophila species. We will use the data from the previous example to study various sequence statistics. In addition, we will see how these distances can be written in a file in various formats through options for page size, precision, and relative placement of distances and their standard errors.

Ex 2.0.1: 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.

Activate the data file Drosophila_Adh.meg using the instructions given in Ex 2.2.1Ex 2.2.3.
We will begin by computing the proportion of nucleotide differences between each pair of Adh sequences.

Ex 2.1.1:Select the Distance|Compute Pairwise command (F7) to display the distance analysis preferences dialog box.

Ex 2.1.2: In the Options Summarytab, click the Model preference pull-down and then select the Nucleotide|p-distance option.

Ex 2.1.3: You may look around at the other options, but at this moment, we will be using the defaults for the remaining options. Click “Compute” to begin the computation.

Ex 2.1.4: A progress indicator will appear briefly, and then the distance computation results will be displayed in grid form in a new window.

We will now compute distances and compare them using other methods.

Ex 2.2.1: Select the Distance|Compute Pairwise command. Use the Models pull-down to select the Nucleotide|Jukes-Cantor method. Now click “Compute” to begin the computation.

Ex 2.2.2: Follow the steps in Ex. 2.1.1- Ex 2.1.3 and compute the Tamura-Nei Distance.

Ex 2.2.3: You should now have open results windows containing the distances estimated by three different methods, which you can now compare.

Ex 2.2.4: After you’ve compared the results, select the File|Quit Viewer option for each result window.

Summary: we have computed nucleotide distances from the nucleotide sequence data in the file Drosophila_Adh.meg.>

Let us now compute the proportion of amino acid differences. Note that MEGA will automatically translate the nucleotide sequences into amino acid sequences using the selected genetic code table.

Ex 2.3.1: Select the Distance|Compute Pairwise command (F7) to display the distance analysis preferences dialog box.

Ex 2.3.2: In the Options Summarytab, click the Models pulldown and then select the Amino Acid|p-distance option.

Ex 2.3.3: Click the “Compute” button to accept the default values for the rest of the options and begin the computation.

Ex 2.3.4: A progress dialog box will appear briefly. As with the previous nucleotide estimation, a results viewer window will be displayed, showing the distances in a grid format.

Ex 2.3.5: After you have inspected the results, use the File|Quit Viewer command to close the results viewer. To shut down MEGA, select the File|Exit menu command from the main MEGA application window and indicate that you would like to close the data file.