Select a species, SAI or group consensus by clicking into its sequence data.
Then check 'Selected' or press 'SET' to restrict the sequence display of all other sequences (i.e. all but the selected sequence) to show only the differences to the selected sequence (aka reference sequence).
Checking 'Follow cursor' will instantly set a new reference sequence, as soon as you set the cursor into a new sequence.
To revert display to standard mode, select 'None'.
CTRL-D: toggles "View differences" mode
CTRL-R: sets reference sequence to the cursor terminal (this only works if "View differences" mode is active, otherwise CTRL-R sets the aligner reference species; see ´The integrated aligners´)
You may define the character used for positions where the displayed sequence does NOT differ from the reference sequence. Default is to display a space, other recommended values are '|' (esp. w/o helix display and smaller seq-spacing), '_', '~', ':' or single quotes.
If 'Mind case?' is checked, characters only differing in case are displayed as differences.
If 'Mind gap type?' is checked, different gaps are displayed as "differences". What is regarded as "gap" may be defined in the text field behind the toggle.