To change the distance metric used to generate the Distance view table, click the Change Analysis Parameters tool ( ) in the Distance view. This opens the Analysis Options dialog where you can specify the Metric and Gap Treatment. Another way to access the same dialog is to use Distance > Parameters.

Use the Gap Treatment drop-down menu to specify when gaps should be ignored. Choices include:

  • Global gap removal – (default) This option ignores any column that contains a gap in any of the aligned sequences in the project. This is the only enabled option for MegAlign Pro projects created prior to the 12.0 release (spring 2014).

  • Pairwise gap removal – This option ignores any column that has a gap in either of the two sequences being compared.

Note that you must press the OK button before MegAlign Pro will initiate the calculation or display new results in the Distance view..

To learn about the other part of this dialog, see Distance metric options.

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