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UP	arb.hlp
UP	glossary.hlp
UP	e4.hlp

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# 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		Sequence color mapping

OCCURRENCE	ARB_EDIT4/Properties/Sequence color mapping

DESCRIPTION	The ARB_EDIT4 editor uses two tables to translate the
		original sequence into a colored displayed sequence:

                First Step:

                      Each character in each sequence is translated into
                      a new character and a color index (0..9) using the definitions
                      from the 'Sequence color mapping' subwindow.

                      - There are different sets (1..8) of color shemes,
                        using two columns for each set.

                      - At the top of the window you may choose which set is used
                        for translation of nucleotides and aminoacids.

                      - The first column shows the characters which should be
                        translated/replaced.

                      - The Nth + 1 column holds the translation instruction for set N.
                        Each of its fields has two characters:

                        - the character which should replace the original value,
                          or '=' if no translation should be performed.

                        - a color index for this character, between 0 and 9.

                        The default for the translation instruction is '=0' 

                Second Step:

                       Each of the color indices (0..9) corresponds to one of
                       the colors defined in <Properties/Change colors & fonts>,
                       namely to

                              index     corresponding color
                              0         SEQUENCES
                              1         HELIX(1)
                              2         COLOR 2
                              3         COLOR 3
                              .         .
                              .         .
                              9         COLOR 9


EXAMPLES	You may use this feature to show:

		- A simplified version of your amino acid alignment.
		- Only YR instead of ACGTU
		- Only ambiguous symbols
		- etc.

BUGS		No bugs known