#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		Column statistic 

OCCURRENCE	ARB_NT/SAI/Create SAI from Sequences/Positional Variability ...

DESCRIPTION	Calculates the base and frequencies positional variability for
		each column independently.
		It uses the parsimony method to find the minimum number of
		mutations for each site.

		The result can be used by:

		-	Parsimony to weight the characters properly
		-	Neighbour joining to estimate the distances
			more accurately.
		-	Filter

		@@@@
		Result:
			'.'	 Less than 10% valid characters
			'0123456789ABCDE...'
				The higher the number the more conserved
				+2 half mutations
				eg .'7' half number of mutations than '5'


NOTES		Use the biggest tree you have.

NOTE		@@@ Compare it to consensus and max frequency.

WARNINGS	if you have only small trees (<100 species), forget this 
		function.

BUGS		No bugs known
