TUTORIAL

In this tutorial, we will show how to create a multiple sequence alignment from sequence data that will be imported into the alignment editor. The protein dataset will be haemoglobin from different organisms, namely:

• Human • Rhesus Macaque • Elephant • Chimpanzee • Baboon • Tarsier

DOWNLOAD AND INSTALL MEGA The link has been provided in the course website sequence download page. After installing the program, click on the icon MEGA from the desktop, or programs menu

IMPORTING THE FASTA FILES • Download the sequences from the link provided in the course website into your computer. These files are in multi fasta file – i.e. one file with several sequences.

• Launch the Alignment Explorer by selecting the Align | Edit/Build Alignment on the launch bar of the main MEGA window. • Select retrieve sequences from a file and click Ok. A dialog will appear asking that allows you to browse to the file to import. • Select the file and click Open.

ALIGNING SEQUENCES USING CLUSTALW • Select the Edit | Select All menu command to select all sites for every sequence in the data set. • Select Alignment | Align by ClustalW from the main menu to align the selected sequences data using the ClustalW algorithm. Click the Ok button to accept the default settings for ClustalW (default penalties, default matrices). • Once the alignment is complete, save the current alignment session by selecting Data | Save Session from the main menu. Give the file an appropriate name.

This will allow the current alignment session to be restored for future editing. • Exit the Alignment Explorer by selecting Data | Exit Aln Explorer from the main menu.

EXPORTING DATA AS FASTA You can export the alignment for further processing - eg phylogenetics. The most widely used format is the

To do this, click on Data | Export alignment | Fasta format and select the target folder to save the alignment.