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#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 the site is.
Stepping 2 position rightwards in the list of given char,
means half number of mutations (eg .'7' means "half number
of mutations compared to '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
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