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
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 2.2.1 – Ex
We will begin by computing the proportion of nucleotide differences between
each pair of Adh
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
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
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
Ex 2.2.4: After you’ve compared the results, select the
File|Quit Viewer option for each result
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.