#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)

# 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		How is the consensus calculated?

OCCURRENCE	ARB_NT/SAI/Create SAI using../Consensus
                ARB_EDIT4/Properties/Consensus definition

DESCRIPTION     What to do with gaps?

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

                     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 column with two 'A's
                            and 500 gaps the program thinks of 100% 'A'.
                            (If the switch is 'on', the relative number of 'A's would be 2%)

                Simplify using IUPAC

                     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.

                     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'.

                     Note:

                        The IUPAC codes are displayed after pressing
                        the 'show IUPAC' button.

                Show as upper or lower case?

                     Define whether the character is displayed in upper or lower case
                     or whether a dot is displayed.

                     Define upper and lower limit:

                            If the percentage of a character is above or equal to the upper
                            limit, the character is displayed in upper case.

                            If the percentage of a character is above or equal to the lower
                            limit and below the upper limit, the character is displayed in lower case.

                            Otherwise a dot ('.') is displayed.

NOTES		None

EXAMPLES	None

WARNINGS	IUPAC symbols in source sequences are ignored.

BUGS		'LINK{consensus.ps}' is broken for more than 10 years
                now. Seems that nobody ever took a look.

