source: tags/arb_5.1/HELP_SOURCE/oldhelp/max_freq.hlp

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#************* 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