9.3.1 Highlighting
Identical or variable sites in an alignment can be highlighted by checking the Highlighting option under the 
Display tab (Figure 9.6
). 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:
- Agreements: Greys out residues that are not identical to the consensus or reference allowing you to quickly locate conserved sites in the alignments.
- Disagreements: This greys out residues that are identical to the consensus or reference in that column, allowing you to quickly locate variable sites in the alignment. Ambiguous disagreements (e.g. G vs N for nucleotides) are also greyed out and not highlighted.
- All Disagreements: This greys out residues that are identical to the consensus or reference in that column, allowing you to quickly locate variable sites in the alignment. Ambiguous disagreements (e.g. G vs N for nucleotides) will not be greyed out, so will appear highlighted.
- Ambiguities: Greys out non-ambiguous residues.
- Gaps: Greys out non-gap positions.
- Transitions/transversions: Greys out residues that are not transitions/transversions compared to the consensus or reference sequence. When highlighting transitions/transversions, it is recommended you turn on the ignore gaps consensus option or some residues may be wrongly highlighted due to the consensus displaying N for sites that contain gaps and non-gaps.
The Go < > 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:
- hold down alt to go to highlighted features in the consensus or reference sequence only.
- hold down ctrl (command) to go to highlighted features that aren’t in the consensus or reference sequence.
- hold down ctrl (command) and alt to go to highlighted features in the currently selected sequence.
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):
- ctrl+D (command+D): Go to next highlighted feature
- ctrl+shift+D (command+shift+D): Go to previous highlighted feature
- ctrl+alt+D (ctrl+option+command+D): Go to next highlighted feature in consensus or reference sequence only
- ctrl+alt+shift+D (ctrl+option+shift+command+D): Go to previous highlighted feature in consensus or reference sequence only
If Use dots is checked, non-highlighted residues are displayed as dots instead of being greyed out.
