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UP	glossary.hlp

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TITLE		Column Statistic (Prototype)

OCCURRENCE	ARB EDITOR

DESCRIPTION	Highlites unlikely bases in an alignment using the maximum
		likelihood technique.
		As soon as the go button is pressed, the selected tree (by
		ARB_NT) and all marked sequences are read. Then the relative
		likelihood for each base is calculated and transformed to
		a number between 0 and 9. This number is translated into a color,
		using the colors 'RANGE 0 ... RANGE 9'. The higher the number,
		the more unlikely a particular base.
		You may improve the output by selecting a valid column statistic,
		which holds information about column dependent rates and base
		frequencies.

NOTES		The colors are not set correctly. Please set different 'CS' colors
		<Props:Sequences: Colors and Fonts> and save them.
		Without a powerfull computer only a small number of sequences can
		be viewed.
		The program assumes that your tree is correct.

WARNINGS	This is only a prototype, don't expect something perfect.
		All sequences which should be analyzed should be marked and
		in the tree shown by ARB_NT !!!!!

BUGS		The colors are not set correctly by default.
		The program can only be started once.

SECTION         Detailed column statistic

                This special mode displays 4 rows below the sequence containing
		the likelihood of each base character.

		Each row consists of two rows of digits displayed in the same color
		(which actually is the color normally used for displaying the
		appropriate base character). The upper of these two rows is the
		first, the lower the second digit of the likelihood.
		[You may like to use the cursor to simplify reading]

		Special character used:
		-----------------------
		SPACE 	= likelihood is 20%
		^	= likelihood is 100%
		?	= can't determine likelihood for that column

		Background colors used:
		-----------------------
		Normally the normal background color is used.

		If a column has a significant likelihood for one base character
		(or for the sum of two base characters), all four rows are
		displayed in color 'Range 0'.

		[significance is 90% (hardcoded) - will be made utilizable soon]

		The single (or two) base character(s) responsive for the
		significance will be displayed in colors 'Range 1' to 'Range 8'
		(the higher the Range-number is, the higher is the likelihood)
