Protocol for using MEGA to generate a 16s rDNA tree for giant panda evolution

Overview:
We will first align the 16s rDNA sequences and then generate a neighor-joining tree.

The steps are illustrated below:

Start MEGA6 software

Click "File" --> "Open A File/Session", Choose "panda_16srDNA.fas". 

 Choose "Align"

Click "Alignment"-->"Align by ClustalW"

Click "OK" to select all sequences, 

Click "OK" to accept the default setting for alignment

Click "No", because 16s rDNA is an RNA coding sequence

Your sequences are now aligned. 

Click "Data" -->"Export Alignment"-->"MEGA Format"

Input an appropriate file name. 

Input an appropriate title: 

Choose "No" because 16s rDNA is not protein-coding gene.

Now, we can start to generate a phylogeny. 

At the main MEGA window, click "Phylogeny" -->"Construct/Test Neighbor-Joining Tree": 

Choose the appropriate alignment file, and then "Open"

Click "Computing" to use the default setting

Generated tree (only partial picture is shown here)

Save your image to use in your lab report.