Distance Matrix

Using the Alignment Editor, you can also create a distance matrix of a multiple sequence alignment.

To create a distance matrix, use the Statistics ‣ Generate distance matrix option in the Actions main menu or in the context menu.

The dialog will appear:

The following parameters are available:

  • Distance algorithm: There are two distance algorithms—“Hamming distance” for dissimilarity and “Simple similarity” for similarity.

  • Profile mode: Counts/Percents — Select the Percents option to display scores as percentages in the report. You can also Exclude gaps if desired.

  • Show group statistics of multiple alignment — Displays group statistics when collapsing is enabled.

  • Save profile to file — Allows saving the profile to a file in HTML or CSV format. The CSV format is convenient for further processing in spreadsheet editors like Excel.

The resulting profile in the HTML mode:

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