This is a simple tutorial, step by step on how to use MEGA file to construct phylogenetic tree (NJ and MP) in MEGA 4 software. To follow these simple steps, you will need to have a ‘MEG file’. I will explain on how to analyse your sequence and how to convert the data into ‘MEG file’ later.
1. Launch the MEGA 4 software
2. Click at ‘click me to activate data file’ or you can click ‘file’ then ‘open data’, or press F5.
3. Choose a data file to analyse, then click ‘open’.
4. MEGA 4 will show you ‘M4: Input Data’, then choose ‘data type’, then click ‘OK’.
5. MEGA 4 will show you ‘confirm’ the click ’Yes’. After that select the genetic code, and then click ‘OK’.
6. You will see a window as picture below. From here, you can try to explore the button at the top of the window, C (conserve sites), V (variable sites), Pi (parsimony informative sites), S (singleton sites) etc… then close the window and back to main MEGA 4 window.
7. to construct a phylogenetic tree (NJ), click ‘phylogeny’, then click ‘bootstrap test of phylogeny’, then click ‘neighbor-joining’.
8. MEGA 4 will show you ‘M4: Analysis Preferences’. Change model to Kimura-2-parameter. Then click ‘Compute’.
9. MEGA 4 will show you the results as below, try to explore and repeat Step 7 for MP tree analysis. Good luck!