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#Please insert up references in the next lines (line starts with keyword UP)
UP arb.hlp
UP glossary.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 Calculate the Percentage of the Most Frequent Base
OCCURRENCE ARB_NT/SAI/create SAI/Max Frequency
DESCRIPTION Finds the most frequent base in each column for all marked
species. Than the number of all sequences with this base are
divided by:
a: the number of all marked sequences, if not ignoring gaps
b: the number of bases in this column, if ignoring gaps
The resulting percentage is divided by ten and the second last
digit taken:
0% - 25% will never occur
25% - 29% -> '2'
30% - 39% -> '3'
...
90% - 99% -> '9'
100% -> '0'
NOTE The result can be used as a conservation profile and filter:
W.L.'s rule:
The higher the number the more conserved the position.
EXAMPLES Say one column contains 7 A's 4 G's and 5 Gaps.
Ignoring Gaps will result in 7/11 == 64 %
which is converted to '6'.
Otherwise we get 7/16 == 44% which will be indicated by a
'4' in the target sequence.
NOTE '-' @#@ are regarded as gaps.
'.' are always ignored.
BUGS No bugs known yet
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