#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)
#SUB	subtopic.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		View differences to selected

OCCURRENCE	ARB_EDIT4/View/View differences ...

DESCRIPTION     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'.

                Key bindings:

                    * 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 LINK{faligner.hlp})

                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.

NOTES		Useful to manually correct alignments.

		The IUPAC field in the top area can be used to guess the sequence 
		data at cursor position.

EXAMPLES	None

WARNINGS	Editing works as usual, even if you do not see what you edit.

BUGS		No bugs known