Overview:

1. First align the sequences in ClustalX.
2. Then output a Neighbor Joining tree based on that alignment to a file.
3. Next use that file as input to DrawTree to generate a nice network of how the sequences are related.

1. Using Notepad create a new file that contains all the sequences you want in the tree in FASTA format, one after the other (see fig.1 right).
   
2. Save the file with a name that indicates the contents. Be sure to save the file in your own teacher folder
   
3. Close Notepad and open ClustalX.

Figure 1

Align Sequences in ClustalX and output a ".ph" Neighbor Joining Tree file.

1. In ClustalX, choose "File" ---> "Load Sequences"
   
2. Then navigate to the folder where you saved your file with all the FASTA format sequences.
   
3. Choose the file. In the example above, the file is called MytilusSpecies_7_ed.txt
   
4. Select "Alignment" ---> "Do Complete Alignment"
   
5. Then select "Trees" --->
   "Output Format Options" and be sure the Output File is set to "Phylip format tree"
   
6. Finally select "Trees" ---> "Draw N-J Tree"
   
7. The program will ask you how you want to save the tree output... Click OK for the default. In our example the output was saved as "MytilusSpecies_7_ed.ph"

Note the ".ph" extension. You will need to copy and rename this file next.

8. Close ClustalX.

Figure 2

Figure 3

1. Highlight the ".ph" file you just created.** and choose "Edit" ---> "Copy"
   
2. Navigate to your "Programs" Folder ---> "Ze_Software" ---> "DrawingTrees"
   
3. Choose "Edit" ---> "Paste"
   
4. "RightClick" on the ".ph" file and rename it "intree" with no extension.