The Tree View shows evolutionary relationships estimated from the multiple sequence alignment, and is calculated using the currently selected Distance metric. The tree is built using the BioNJ algorithm (Gascuel, 1997), a variant of the Neighbor-Joining algorithm (Saito and Nei, 1987) used in MegAlign. The following video is a brief overview of the Tree view:

Selections within the Tree view are synchronized with other views in MegAlign Pro. Similarly, selections made elsewhere will be highlighted simultaneously in the Tree View.

The Tree view is only accessible after you have performed a multiple alignment, and becomes inaccessible again if you unalign the sequences. After performing an alignment, you can access the view by clicking on the Tree tab (the dark blue part of the image, below).

Branch lengths are displayed, by default, and a distance scale appears at the bottom left of the image. Phylogenetic trees are considered to be reflections of the evolutionary relationships between the aligned sequences. Due to the nature of the tree-building algorithm, note that the sum of branch lengths between any pair of sequences is not expected to equal the pair-wise distance reported in the Distance view. This is because the computed branch lengths are conditioned by the relationships to other sequences represented on the tree.

Above the tree is a row containing the following information:

  • Block – (multi-block Mauve alignments only) The color of the alignment block currently selected in the Overview.
  • Clustering – The clustering method used is BioNJ (Gascuel, 1997).
  • Sequences – Number of sequences in the alignment or in the active block.
  • Residues considered – Total length of alignment minus all columns containing even a single gap. This field shows both the minimum and maximum number of residues considered, if they differ.

Changes made to the alignment (e.g., realigning with a different method, or with additional sequences) or to the distance metric cause the tree to be recalculated.

In certain situations, it may not be possible to calculate distances for every pair of aligned sequences. In these cases, sub-clusters of related sequences may be shown together on separate trees, or listed together as a single node. See Distance view for more information.


The following table describes ways to control the appearance of the Tree view:

Task How to…
To change settings related to the Tree view Use the Tree section of the Style panel.
To redraw the tree according to the default settings Use Tree > Reset Phylogenetic Tree View or Ctrl/Cmd+Shift+R.

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