This project was prepared as part of a BioQUEST faculty development workshop entitled BioQUEST 2004 Summer Workshop for Undergraduate Faculty: Systems Biology at Beloit College in June 2004. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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The Phylogenetic Tree Constructor
Authors          Audiences          Overview           Materials          Resources           Future Directions



Barry Hennig
Massey University, Palmerston North Campus

Timothy Denton
Los Angeles Trade Technical College

Brian White
University of Massachusetts


Possible Audiences:

  • High School
  • College


Brief Overview:

The Phylogenetic Tree Constructor
The Phylogenetic Tree Constructor (PTC) is an easy-to-use web-based interface that students can use to explore molecular phylogeny within a defined set of DNA or protein sequences.

The PTC presents the student with a choice of "Main Tree Organisms". She then selects the organisms she would like to explore from these lists. This is shown below.

She then selects a single "Outgroup" organism as shown below and submits the selections to the server:

The server then generates an alignment of the selected sequences:

The server then generates two kinds of phylogenetic trees based on the alignment.

  • Distance-Matrix: where the map is calculated based on the number of differences between the various sequences. This method allows the students to calculate the time since the last common ancestor using a "Molecular Clock".
  • Discrete-Character: where the map is calculated using the specific distances via a maximum parsimony algorithm. Although this does not generate "Molecular Clock" data, the relationships shows by these trees are considered to be more accurate than those from the Distance Matrix trees.

The collection of sequences is selected by the instructor and customized for a particular task. Specific examples are listed below. Instructions for preparing the sequence file are available here.

The sequence file and the script, along with several accessory and program files must be housed on a web-server. The script file, which contains setup information, is available here.

A sample sequence file can be found here.  


Project Materials:

  • The Original Phylogenetic Tree Constructor. It uses cytochrome c protein sequences from animals and plants.
  • The New Phylogenetic Tree Constructor. It uses cytochrome c protein sequences from animals and plants.
  • Construct Trees of Ferns using several DNA sequences.
  • Construct Trees of Flu-viruses using DNA sequences of a viral gene.
  • Construct Trees of Animals using hemoglobin protein sequences.
  • Construct Trees of Vertebrates using cytochrome c oxidase subunit 1 protein sequences.



- MainTree.gif
- OutGroup.gif
- JalviewAlign.gif
- JalviewTree.gif
- ParsimonyTree.gif
- making_files.pdf
- sequences.txt
- sequences.txt