Phylogenetic Tree Diagrams

Making Phylogenetic Tree Diagrams

Angelique Bosse
Montgomery Blair High School
Silver Spring, Maryland 20901

Go to Biology Workbench at http://workbench.sdsc.edu/
Click "Enter the Biology Workbench 3.2" and enter user name and password, click "ok" (or set up a free account first)
Scroll down and click "Protein Tools"
Select "Ndjinn- Multiple Database Search"
Click "Run"
In the skinny white box next to "Exact Match" type in a protein such as "beta hemoglobin" and select "Show All Hits"
Scroll down to choose a database such as "SWISSPROT- Swissprot Database" by clicking in white box
Go back up to top of screen and click "Search"
Result is a list of "hits" for your requested protein under "Matching Database Record". Hits include the protein sequences from a variety of organisms
Select six unrelated species' beta hemoglobin proteins (such as chick, sheep, horse, bovine, pig) by highlighting each
Import the selected sequences by clicking "Import Sequence(s)"
From the menu select "CLUSTALW- Multiple Sequence Alignment"
Click the little white box next to your chosen 6 sequences to analyze
Click "Run"
On the next screen, scroll down and click "Submit"
On the next screen, click "Import Alignment(s)"
From the menu select "DRAWTREE- Draw Unrooted Phylogenetic Tree from Alignment"
Click lower white box next to "CLUSTALW-protein" and your six selected sequences
Click "Run"
Scroll down, click "Submit"
Scroll down to see the tree
Click "Return"
From the menu, select "DRAWGRAM- Draw Rooted Phylogenetic Tree form Alignment"
Be sure the white box next to "CLUSTALW- protein" is checked
Click "Run"
On the next screen, click "Submit"
Scroll down to see the tree
Click "Return"

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