9.3.1 Highlighting

Identical or variable sites in an alignment can be highlighted by checking the Highlighting option under the PIC Display tab. The drop down menus allow you to choose what to highlight, and whether the consensus or reference sequence should be used for the comparison. The options for what to highlight are:

The Go to previous/next arrows allow you to navigate forwards and backwards between highlighted features. Where there are more than two consecutive highlights within a sequence the selection will only stop on the first and last of these. Using the drop down menu, you can choose to navigate between highlighted features in any sequence, in the current sequence, in a different column, or the reference/consensus sequence.

When clicking the arrows:

These actions may also be accessed directly using specific shortcuts which can be configured from Tools Preferences Keyboard. Using a keyboard shortcut or modifier key will override what is set in the drop down menu.

Default Shortcuts (mac keys in brackets):

If Use dots is checked, non-highlighted residues are displayed as dots instead of being greyed out.