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

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

# 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		Consensus

OCCURRENCE	ARB_NT/SAI/Consensus

DESCRIPTION	Calculates consensus for marked or all sequences.

		1. Choose an 'alignment' (see LINK{glossary.hlp}) from the
			'Alignment' subwindow.

		2. Define whether 'marked' (see LINK{glossary.hlp}) or all
			sequences should be used by pressing the respective
			checkbox after the 'species' prompt.

		3. Define whether to use or to ignore gaps entirely. If you count
			gaps and the gap frequency exceeds 'threshold for gaps', the
			result will be shown as '-'. If the switch is 'off',
			the algorithm will virtually remove all gaps.
			That means if you have a coloumn with two 'A's
			and 500 gaps the program thinks
			of 100% 'A'. If the switch would be 'on', the relative
			number of 'A's would be 2%.

		4. Define whether the most frequent base or the IUPAC code
			(more then one base) should be shown at the particular
			position by pressing the respective checkbox after the
			'simplify' prompt.
			The IUPAC codes are displayed after pressing the <show
			IUPAC> button.
			Characters are used for IUPAC encoding only if their
			frequency exceeds 'threshold for character'.
			Example:
			If you have 40% 'A', 10% 'C', 40% 'G' and 10% 'T' and
			'threshold for character' is set to 20%, the
			program looks for a iupac code only for 'A' and 'G'.

		5. Define a name for the consensus sequence by selecting one
			from the 'SAI' subwindow or by typing it to the
			'Name of New SAI' field.

NOTES		The consensus sequence is stored within the database as an 'SAI'
		entry and automatically edited with 'ARB_EDIT'.

		Display detailed help in postscript format by choosing
		'Postscript: Consensus.ps' from the 'Main Topic' subwindow.

		If a column contains only gaps the result will be shown as '='.

EXAMPLES	None

BUGS		Our postscript viewer cannot show 'Postscript: Consensus.ps'
		You may print it on your printer: $ARBHOME/lib/ps/Consensus.ps


BUGS		IUPAC symbols in source sequences are ignored.