Phylogeny lab, west nile virus using envelop glycoprotein squences

Download MEAG from www.megasoftware.net
This menu is written for a Windows computer.  Toolbar features are slightly different in Mac.

Open file "WNV.mas" with MEGA.  (In Mac, you need to start MEGA first, and then look for this file.)

In "Alignment Explorer", click "Translated Protein Sequences"

 Click "Yes" for selection and genetics tables.

 Translated proteins should look like this

Choose "Alignment" by "Align by ClustalW"

"OK" to use the default alignment setting.

Click "Data" -> "Export Alignment" -> "MEGA format".

Input title for the alignment

This alignment are for "protein coding sequences". 

In the main window of MEGA, choose "Phylogeny" -> "Construct/Test Neighbor-Joining Trees"

Choose default parameters.

We should be able to see the generated tree.

In order to save the image, we can "Image"->"Copy to Clipboard".

And then "Paste" to a WORD document. 

Note: Please feel free to explore many other features of MEGA. 

Reference:
Online MEGA help file, http://www.megasoftware.net/webhelp/helpfile.htm