1. Multiple Sequence Alignments

1.1. Getting started with MEGA


There is an excellent tutorial on the MEGA site and this is excerpt of the tutorial for the exercise.

1.1.1. How to make an alignment using MEGA

Step 1:Open MEGA software and you will see a screen like in the following figure:
Step 2:Click on the small arrow on the “Align” tab
Step 3:Click on ‘Edit/Build alignment’
Step 4:Select a new alignment.
Step 4:Select protein
Step 5:From file open, select “seq_align2.fasta” and open file.
Step 6:From Edit, select all sequences. To do an alignment using Muscle, click on Muscle tab.
Step 7:Use default options and perform an alignment. To learn more about the options, go to the MEGA manual.

1.1.2. Edit the alignments

Step 1:You can insert gaps, delete blocks, and delete residues.

Be very careful when you edit a sequence alignment. It should be biologically meaningful.


1.1.3. Exporting MSA

Mega allows to export the MSA in different formats.