Click to see a video demo of how to build a phylogenetic tree by BSW.

Step 1. Enter the Biology Student Worbench, or BSW.
The BSW contains all the bioinformatics tools that we will need to perform all steps of this exercise. Follow these steps to get started.

1. Go to the Biology student workbench website
2. Click on Use Student Workbench website and go to Student Interface to Biology Workbench.
3. To enter the workbench type Userid: beckman_oh, password: user
4. Select Session Tools
5. Select the session name: exercise1
6. Click on Resume Session and then on Run, go to that session.

7. Click on Protein Tools.



Step 2. Collect sequences.
If we want to construct a phylogenetic tree we need to compare sequences that come from the same particular segment of DNA common to ALL organisms. Figure 2 shows the FASTA records of the sequences that we are going to compare. We have placed these records in the BSW. Scroll to the bottom of the screen and select all five sequences.



Step 3. Align all sequences and Calculating evolutionary distance.
To estimate when those organisms may have diverged from a common ancestor, we need to compare how different from each other the sequences are. The alignment tools in the BSW align and calculate the evolutionary distances between sequences.

1. ClustalW is one of the tools that will align all the sequences. To select this tool, scroll down the list until you see the name, then click on it.

2. Another page will appear with some parameters that you can change if you want. Just click Sumbit.
3. When the results are displayed, scroll down to examine the results. You will see the aligned sequences, the tree, and the distances between pairs of sequences click continue with the next step of the exercise and click Import Alignment(s).


Step 4. Build the tree.
All tools in the BSW require that you align the sequences first; since they need the information of the evolutionary distances in order to build the trees.

1. Make sure that Alignment Tools is selected

2. Select the alignment "ClustalW - Protein seq_org1,seq_org2, seq_org3,seq_org4,seq_org5"

3. Click on DRAWGRAM located inside the box, Drawgram is a tool that will draw the tree.

4. When the screen with the results shows up, scroll down to see the tree.

5. Click on Return to exit this screen and end the exercise.