Making Phylogenetic Tree Diagrams  

Angelique Bosse
Montgomery Blair High School
Silver Spring, Maryland 20901

  • Go to Biology Workbench at
  • 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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