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X11 is a program that comes with MacOS X and is essential for displaying the Wine and Wineskin versions of MEGA (MEGA7 and earlier) on the Mac. If you close X11 MEGA will close as well.

In this example we compute various distances for the Adh sequences from 11 Drosophila species (Thomas and Hunt 1993). We used this data in the previous example to study various sequence statistics. In addition, you will be 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.

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Ex 1/3.4Since this data file does not contain any errors, no error messages are flashed. Do you see any change on the screen? A box labeled Current Data appears that contains information about the input data just activated for analysis. A Selections box also appears on the screen that informs you regarding the current analysis methods chosen.

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The number in the matrix indicates the number of common sites between sequences that are available for analysis. When this number is zero, there are no common sites. To get around this problem, you may want to eliminate some sequences. In addition, the use of the "Pairwise-Deletion" option for handling alignment gaps and missing data may also be employed.

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The sequences are then displayed on the screen. Ex 2/3.2DNA sequences are displayed on the screen with the cursor on the first site of the first sequence. Use the right arrow ( ® ) and left arrow ( ¬ ) keys to move from site to site and note a change in the Site# display in the bottom-right corner. Use the up ( ­ ) and down ( ¯ ) arrow keys to move between OTUs and note changes in the OTU Name view on the top panel.

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Just Enter (or click on the OK button). Ex 4/1.3A status report box informs that the data are being read. At this stage, the program inquires whether the nucleotide sequence data are from a coding or noncoding gene. Select the noncoding mode by pressing the N key. The Current Data and the Selection windows appear on the screen.

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  • However, it is not permissible to redistribute MEGA in any form to other users
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In this example, you will find the same tree as that obtained by the branch-and-bound method if you use the default option (search factor equal to 2 for all steps of OTU addition). However, the computational time will be much shorter.

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In this file, sequences are arranged in the interleaved (block-wise) format. Note that the antigen recognition sites (ARS) are marked in comments.

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In this exercise the use of the Data|Data Presentation command for computing various statistical quantities of nucleotide sequences is illustrated. In addition, short-cuts for frequently used commands, method of accessing on-line helps, and the reason why some commands are enabled and others are disabled are explained.

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The distance file will appear on the screen in a double line bordered window. Press F1, the help key, to activate the help, and after a quick glance at the help text, press Esc or click on the filled square icon on the top left corner to put the help window away.

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In MEGA (see) this test is available for the p-distance, Jukes-Cantor distance, and Kimura's 2-parameter (s + v) distance for nucleotide sequences. Since we did the above analysis for the Jukes-Cantor distance, we will use the same distance estimation method to compare the results from the bootstrap and standard error tests. Since the Selections box shows that Jukes-Cantor distance and NJ tree making method are already selected.

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This brings a status report box with a message. The neighbor-joining tree will soon appear on the screen. Ex 4/2.4At this moment, you are automatically put into the phylogenetic-tree editor. This editor provides operations in two modes: view mode and edit mode. The edit mode can be recognized by the presence of a blinking cursor. By default you are placed in the view mode.

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As an exercise, you may try to examine this data set on the screen by using that command. Just press F4, the hot-key for the Data Presentation command, and you will see the data on the screen.

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Soon after, the program inquires whether the data is protein-coding or not. Press the Y key to select the Protein-coding option. For the genetic code table to be used, select the "Universal" option, and press Enter. The Current Data and the Selection boxes appear on the screen.