The Distance view shows a matrix (i.e., table) of numbers representing distances computed for each pair of sequences for the selected aligned block. Sequence distances are used as input in creating the phylogenetic tree shown in the Tree view. Selections within the Distance view are synchronized with other views in MegAlign Pro. Similarly, selections made elsewhere will be highlighted simultaneously in the Distance view.

The Distance 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 Distance tab.

Above the matrix is a row containing the following information:

  • Block – (multi-block Mauve alignments only) The color of the alignment block currently selected in the Overview.
  • Sequences – The number of sequences in the alignment or in the active block.
  • Global/Pairwise gap removal – The gap treatment specified in the Distance section.
  • 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.


Here are some tips for understanding the information shown in the matrix:

  • Larger numbers correspond to greater differences between sequences. Uncorrected distances are always ≤1.0. However, the Kimura and Tamura-Nei values can exceed 1.0 because they reflect the inferred actual number of nucleotide substitutions or amino acid replacements per site, not the observed distance.
  • The upper and lower triangles of the matrix are reflections of one other and contain the same information.
  • No numbers appear on the diagonal, since a sequence cannot differ from itself.
  • In certain situations, it may not be possible to calculate distances for every pair of aligned sequences, in which case “NA” is displayed. In other cases, “NA” may be an artifact of the computational algorithm; for example, an attempt to calculate the log of a negative number.
  • When the divergence between a pair of sequence is greater than about 0.75, it may not be possible to calculate a value for corrected distance using the Kimura and Tamura-Nei metrics.


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

Task How to…
To change settings related to the Distance view Use the Distance section of the Style panel.
To display a tool tip with the name of the sequence corresponding to a cell Hover over any row/column header or any cell on the diagonal of the matrix.

To display a tool tip with the the two sequence names and the distance between them Hover over a distance cell in the table that is not on the diagonal. For projects using Pairwise gap removal (see Distance section), the tool tip also contains the number of residues considered for that pair.
To select all cells in the table Choose Distance > Table > Select All.
To use editing commands with the Distance table Choose Distance > Table > Copy (Select All, Rename, Rename with Fields).
To freeze scrolling Choose Distance > Table > Freeze Scrolling Region. In a large table, this command allows you to compare rows near the top with those further down.

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