Gap treatment options affect the calculation of distances, which, in turn, affect the Distance and Tree views. One of two options may be specified in the Distance section of the Style panel. To open the section, click on the expand bar entitled Distance, or choose View > Style > Distance.

Use the Gap Treatment drop-down menu to choose between these options:

  • 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.

The banners at the tops of the Distance and Tree views will show a range in the field Residues considered if different numbers of residues are considered for different pairs of sequences. This happens frequently when Pairwise gap removal is checked. However, if the minimum and maximum values differ greatly, we recommend selecting Global gap removal instead.

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