The Tree view shows evolutionary relationships predicted from the multiple sequence alignment, and is built using the BioNJ algorithm (Gascuel, 1997), a variant of the Neighbor-Joining algorithm (Saito and Nei, 1987). Selections within this view are synchronized with all views in MegAlign Pro.

  1. To display the Tree view, click on the Tree tab at the bottom of the MegAlign Pro window.

The Tree view is calculated using the current Distance metric. In Part D, you chose the Kimura distance metric, so this is the metric on which the current Tree view is based.

  1. If necessary, use the horizontal or vertical zoom sliders to make the entire phylogenetic tree visible.

Note that the MegAlign Pro tree is always unrooted, regardless of the methods used for the multiple alignment and distance calculations.

  1. Experiment with the settings in the Style panel’s Tree section on the right to see how these changes affect the look of the Tree view.

    • Change the Layout by clicking any of the four position icons at the top of the Tree section.

    • Change the font style and/or size used for the Leaves using the middle drop-down menu and text box.

    • Add a background color for the text, if desired, by checking the Background checkbox, then clicking on the white box on the right to make a selection from the color picker.

    • Change the color of the branches by clicking on the Branches Color box and making a selection from the color picker.

    • Show or hide the branch length by checking and unchecking the corresponding box. While the box is checked, try adjusting the number of Decimal places.
  1. In the Distance section on the right, select a different distance Metric. Observe how the Tree view changes.

While the Kimura and Scoredist metrics yield almost identical trees, Uncorrected Pairwise Distance pairs one of the mice with "human," rather than with the other mouse. For greatest accuracy, we recommend using an evolutionarily adjusted metric (e.g., Kimura or Scoredist) whenever possible.

  1. If desired, save the project using File > Save, or by clicking on the Save tool ().

This is the end of the Clustal Omega alignment tutorial.

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